Evaluating Antibiotic Resistance Gene Correlations with Antibiotic Exposure Conditions in Anaerobic Membrane Bioreactors

Zarei-Baygi, Ali; Harb, Moustapha; Wang, Phillip; Stadler, Lauren B.; Smith, Adam L.

doi:10.1021/acs.est.9b00798

Cited by 97 publications

(32 citation statements)

References 65 publications

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“…qPCR assays, on the other hand, are limited by the number of targets they can include. ARG studies that employ qPCR, for example, commonly target between 5 and 20 genes per sample (26,(37)(38)(39). Although qPCR arrays have increased the throughput of qPCR and provided valuable insights on ARG profiles (28,40), qPCR arrays without standard curves do not deliver absolute concentrations, are subject to the same primer specificity limitations as traditional qPCR, and are similarly limited by available knowledge on ARGs at the time of qPCR array design.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic Quantification of Genes with Internal Standards

Crossette

Gumm

Langenfeld

et al. 2021

mBio

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We demonstrate that an assembly-independent and spike-in facilitated metagenomic quantification approach can be used to screen and quantify over 2,000 genes simultaneously, while delivering absolute gene concentrations comparable to those for quantitative PCR (qPCR). DNA extracted from dairy manure slurry, digestate, and compost was spiked with genomic DNA from a marine bacterium and sequenced using the Illumina HiSeq4000. We compared gene copy concentrations, in gene copies per mass of sample, of five antimicrobial resistance genes (ARGs) generated with (i) our quantitative metagenomic approach, (ii) targeted qPCR, and (iii) a hybrid quantification approach involving metagenomics and qPCR-based 16S rRNA gene quantification. Although qPCR achieved lower quantification limits, the metagenomic method avoided biases caused by primer specificity inherent to qPCR-based methods and was able to detect orders of magnitude more genes than is possible with qPCR assays. We used the approach to simultaneously quantify ARGs in the Comprehensive Antimicrobial Resistance Database (CARD). We observed that the total abundance of tetracycline resistance genes was consistent across different stages of manure treatment on three farms, but different samples were dominated by different tetracycline resistance gene families. IMPORTANCE qPCR and metagenomics are central molecular techniques that have offered insights into biological processes for decades, from monitoring spatial and temporal gene dynamics to tracking ARGs or pathogens. Still needed is a tool that can quantify thousands of relevant genes in a sample as gene copies per sample mass or volume. We compare a quantitative metagenomic approach with traditional qPCR approaches in the quantification of ARG targets in dairy manure samples. By leveraging the benefits of nontargeted community genomics, we demonstrate high-throughput absolute gene quantification of all known ARG sequences in environmental samples.

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Section: Discussionmentioning

confidence: 99%

Metagenomic Quantification of Genes with Internal Standards

Crossette

Gumm

Langenfeld

et al. 2021

mBio

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“…Multidrug-resistant (MDR) strains arise because exposition to antimicrobial compound (AMC) in the environment selects them ( Vuotto et al, 2018 ; Sanderson et al, 2020 ), as well as horizontal AMC gene transfer ( Zarei-Baygi et al, 2019 ) through MGE ( Baker et al, 2018 ). This relation between ARG and MGE is difficult for the therapy of MDR bacterial infections ( Vuotto et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Identification and Characterization of the CRISPR/Cas System in Staphylococcus aureus Strains From Diverse Sources

et al. 2021

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The CRISPR-Cas [clustered regularly interspaced short palindromic repeats and the CRISPR-associated genes (Cas)] system provides defense mechanisms in bacteria and archaea vs. mobile genetic elements (MGEs), such as plasmids and bacteriophages, which can either be harmful or add sequences that can provide virulence or antibiotic resistance. Staphylococcus aureus is a Gram-positive bacterium that could be the etiological agent of important soft tissue infections that can lead to bacteremia and sepsis. The role of the CRISPR-Cas system in S. aureus is not completely understood since there is a lack of knowledge about it. We analyzed 716 genomes and 1 genomic island from GENOMES-NCBI and ENA-EMBL searching for the CRISPR-Cas systems and their spacer sequences (SSs). Our bioinformatic analysis shows that only 0.83% (6/716) of the analyzed genomes harbored the CRISPR-Cas system, all of them were subtype III-A, which is characterized by the presence of the cas10/csm1 gene. Analysis of SSs showed that 91% (40/44) had no match to annotated MGEs and 9% of SSs corresponded to plasmids and bacteriophages, indicating that those phages had infected those S. aureus strains. Some of those phages have been proposed as an alternative therapy in biofilm-forming or infection with S. aureus strains, but these findings indicate that such antibiotic phage strategy would be ineffective. More research about the CRISPR/Cas system is necessary for a bigger number of S. aureus strains from different sources, so additional features can be studied.

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“…Antibiotic resistance genes were studied in an aerobic membrane bioreactor to determine if the influent antibiotics are changing the genes within the bioreactor (Zarei‐Baygi, Harb, Wang, Stadler, & Smith, 2019). Results shows that the genes did change with different antibiotics in the influent.…”

Section: Microconstituentsmentioning

confidence: 99%

Membrane processes

Arabi¹,

Pellegrin

Aguinaldo

et al. 2020

Water Environment Research

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This literature review provides a review for publications in 2018 and 2019 and includes information membrane processes findings for municipal and industrial applications. This review is a subsection of the annual Water Environment Federation literature review for Treatment Systems section. The following topics are covered in this literature review: industrial wastewater and membrane. Bioreactor (MBR) configuration, membrane fouling, design, reuse, nutrient removal, operation, anaerobic membrane systems, microconstituents removal, membrane technology advances, and modeling. Other subsections of the Treatment Systems section that might relate to this literature review include the following: Biological Fixed-Film Systems, Activated Sludge, and Other Aerobic Suspended Culture Processes, Anaerobic Processes, and Water Reclamation and Reuse. This publication might also have related information on membrane processes: Industrial Wastes, Hazardous Wastes, and Fate and Effects of Pollutants.

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Evaluating Antibiotic Resistance Gene Correlations with Antibiotic Exposure Conditions in Anaerobic Membrane Bioreactors

Cited by 97 publications

References 65 publications

Metagenomic Quantification of Genes with Internal Standards

Metagenomic Quantification of Genes with Internal Standards

Identification and Characterization of the CRISPR/Cas System in Staphylococcus aureus Strains From Diverse Sources

Membrane processes

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