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Article: Effects of sample preservation and DNA extraction on enumeration of antibiotic resistance genes in wastewater

TitleEffects of sample preservation and DNA extraction on enumeration of antibiotic resistance genes in wastewater
Authors
Keywordsantibiotic resistance genes
DNA extraction
global comparison
wastewater treatment
metagenomics
Issue Date2018
PublisherOxford University Press. The Journal's web site is located at http://femsec.oxfordjournals.org/
Citation
FEMS Microbiology Ecology, 2018, v. 94 n. 2, p. article no. fix189 How to Cite?
AbstractWith the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move toward standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit and ZR Fecal DNA MiniPrep), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA. Annotated sequences obtained from the DNA extracted using the three kits shared similar taxonomy and ARG profiles. Overall, it was found that the DNA yield and purity, and diversity of ARGs captured were all highest when applying the FastDNA SPIN Kit for Soil for all three WWTP sample types investigated here (influent, activated sludge, effluent). Quantitative polymerase chain reaction of 16S rRNA genes confirmed the same trend as DNA extraction yields and similar recovery of a representative Gram-negative bacterium (Escherichia coli). Moreover, sample fixation in ethanol, deep-freezing and overseas shipment had no discernable effect on ARG profiles, as compared to fresh samples. This approach serves to inform future efforts toward global comparisons of ARG distributions in WWTPs.
DescriptionLink to Free access
Persistent Identifierhttp://hdl.handle.net/10722/293561
ISSN
2019 Impact Factor: 3.675
2015 SCImago Journal Rankings: 1.687
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLi, AD-
dc.contributor.authorMetch, JW-
dc.contributor.authorWang, Y-
dc.contributor.authorGarner, E-
dc.contributor.authorZhang, AN-
dc.contributor.authorRiquelme, MV-
dc.contributor.authorVikesland, PJ-
dc.contributor.authorPruden, A-
dc.contributor.authorZhang, T-
dc.date.accessioned2020-11-23T08:18:34Z-
dc.date.available2020-11-23T08:18:34Z-
dc.date.issued2018-
dc.identifier.citationFEMS Microbiology Ecology, 2018, v. 94 n. 2, p. article no. fix189-
dc.identifier.issn0168-6496-
dc.identifier.urihttp://hdl.handle.net/10722/293561-
dc.descriptionLink to Free access-
dc.description.abstractWith the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move toward standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit and ZR Fecal DNA MiniPrep), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA. Annotated sequences obtained from the DNA extracted using the three kits shared similar taxonomy and ARG profiles. Overall, it was found that the DNA yield and purity, and diversity of ARGs captured were all highest when applying the FastDNA SPIN Kit for Soil for all three WWTP sample types investigated here (influent, activated sludge, effluent). Quantitative polymerase chain reaction of 16S rRNA genes confirmed the same trend as DNA extraction yields and similar recovery of a representative Gram-negative bacterium (Escherichia coli). Moreover, sample fixation in ethanol, deep-freezing and overseas shipment had no discernable effect on ARG profiles, as compared to fresh samples. This approach serves to inform future efforts toward global comparisons of ARG distributions in WWTPs.-
dc.languageeng-
dc.publisherOxford University Press. The Journal's web site is located at http://femsec.oxfordjournals.org/-
dc.relation.ispartofFEMS Microbiology Ecology-
dc.rightsPre-print: Journal Title] ©: [year] [owner as specified on the article] Published by Oxford University Press [on behalf of xxxxxx]. All rights reserved. Pre-print (Once an article is published, preprint notice should be amended to): This is an electronic version of an article published in [include the complete citation information for the final version of the Article as published in the print edition of the Journal.] Post-print: This is a pre-copy-editing, author-produced PDF of an article accepted for publication in [insert journal title] following peer review. The definitive publisher-authenticated version [insert complete citation information here] is available online at: xxxxxxx [insert URL that the author will receive upon publication here].-
dc.subjectantibiotic resistance genes-
dc.subjectDNA extraction-
dc.subjectglobal comparison-
dc.subjectwastewater treatment-
dc.subjectmetagenomics-
dc.titleEffects of sample preservation and DNA extraction on enumeration of antibiotic resistance genes in wastewater-
dc.typeArticle-
dc.identifier.emailZhang, T: zhangt@hkucc.hku.hk-
dc.identifier.authorityZhang, T=rp00211-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/femsec/fix189-
dc.identifier.pmid29300934-
dc.identifier.scopuseid_2-s2.0-85054344426-
dc.identifier.hkuros319374-
dc.identifier.volume94-
dc.identifier.issue2-
dc.identifier.spagearticle no. fix189-
dc.identifier.epagearticle no. fix189-
dc.identifier.isiWOS:000428122100016-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl0168-6496-

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