Loading…
High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria
The emergence of bacterial pathogens that are resistant to clinical antibiotics poses an increasing risk to human health. An important reservoir from which bacterial pathogens can acquire resistance is the human gut microbiota. However, thus far, a substantial fraction of the gut microbiota remains...
Saved in:
Published in: | PloS one 2019-01, Vol.14 (1), p.e0210970-e0210970 |
---|---|
Main Authors: | , , , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that this one cites Items that cite this one |
Online Access: | Get full text |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
cited_by | cdi_FETCH-LOGICAL-c743t-a003e3e2eff073173001788d8d5077aece7ff42d270163b5f43c42f88e2572be3 |
---|---|
cites | cdi_FETCH-LOGICAL-c743t-a003e3e2eff073173001788d8d5077aece7ff42d270163b5f43c42f88e2572be3 |
container_end_page | e0210970 |
container_issue | 1 |
container_start_page | e0210970 |
container_title | PloS one |
container_volume | 14 |
creator | Versluis, Dennis de J Bello González, Teresita Zoetendal, Erwin G Passel, Mark W J van Smidt, Hauke |
description | The emergence of bacterial pathogens that are resistant to clinical antibiotics poses an increasing risk to human health. An important reservoir from which bacterial pathogens can acquire resistance is the human gut microbiota. However, thus far, a substantial fraction of the gut microbiota remains uncultivated and has been little-studied with respect to its resistance reservoir-function. Here, we aimed to isolate yet uncultivated resistant gut bacteria by a targeted approach. Therefore, faecal samples from 20 intensive care patients who had received the prophylactic antibiotic treatment selective digestive decontamination (SDD), i.e. tobramycin, polymyxin E, amphotericin B and cefotaxime, were inoculated anaerobically on porous aluminium oxide chips placed on top of poor and rich agar media, including media supplemented with the SDD antibiotics. Biomass growing on the chips was analysed by 16S rRNA gene amplicon sequencing, showing large inter-individual differences in bacterial cultivability, and enrichment of a range of taxonomically diverse operational taxonomic units (OTUs). Furthermore, growth of Ruminococcaceae (2 OTUs), Enterobacteriaceae (6 OTUs) and Lachnospiraceae (4 OTUs) was significantly inhibited by the SDD antibiotics. Strains belonging to 16 OTUs were candidates for cultivation to pure culture as they shared ≤95% sequence identity with the closest type strain and had a relative abundance of ≥2%. Six of these OTUs were detected on media containing SDD antibiotics, and as such were prime candidates to be studied regarding antibiotic resistance. One of these six OTUs was obtained in pure culture using targeted isolation. This novel strain was resistant to the antibiotics metrodinazole and imipenem. It was initially classified as member of the Ruminococcaceae, though later it was found to share 99% nucleotide identity with the recently published Sellimonas intestinalis BR72T. In conclusion, we show that high-throughput cultivation-based screening of microbial communities can guide targeted isolation of bacteria that serve as reservoirs of antibiotic resistance. |
doi_str_mv | 10.1371/journal.pone.0210970 |
format | article |
fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_2168161386</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A569978623</galeid><doaj_id>oai_doaj_org_article_28d5ad10ea8f4e44a5d74b62ea379356</doaj_id><sourcerecordid>A569978623</sourcerecordid><originalsourceid>FETCH-LOGICAL-c743t-a003e3e2eff073173001788d8d5077aece7ff42d270163b5f43c42f88e2572be3</originalsourceid><addsrcrecordid>eNqNk89u1DAQxiMEolB4AwSWkBAcdnHsJM5yQKoqoJUqVeLf1Zo4k8SV1w6205an4JVxdrdVF_WAcnA0_s03ns-eLHuR02XORf7-wk3eglmOzuKSspyuBH2QPclXnC0qRvnDO_8H2dMQLigteV1Vj7MDTquSl4I_yf6c6H4gcfBu6odxikRNJupLiNrZRQMBWxKUR7Ta9sRZMrpEBgJmWms7rYm71i0SNehxDhp3FUgE32NMiTo4sxEiriNgo260i1oRj0GHmAJkmNZgSZ_KNqAieg3PskcdmIDPd-th9uPzp-_HJ4uz8y-nx0dnCyUKHhdAKUeODLuOCp4LTmku6rqt25IKAahQdF3BWiZoXvGm7AquCtbVNbJSsAb5YfZqqzsaF-TOyyBZXtV5lSebEnG6JVoHF3L0eg3-t3Sg5SbgfC_Bp3YMSpbKQptThLorsCigbEXRVAyBixUvZ60PW60r6DdWopUWvNJhI2h042fxq8lLa-ZlnJogy0Jskz_ujjo1a2wV2ujB7J1of8fqQfbuUlacV6wSSeDtTsC7XxOGKNc6KDQGLKbLTE2LVUGpqFlCX_-D3m_Njuohda9t51JdNYvKo7JarURdMZ6o5T1U-lpca5VebadTfC_h3V5CYiJexx6mEOTpt6__z57_3Gff3GEHBBOH9DSn-WmGfbDYgsq7EDx2tybnVM5Dd-OGnIdO7oYupb28e0G3STdTxv8C_Q8sBA</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2168161386</pqid></control><display><type>article</type><title>High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria</title><source>Publicly Available Content Database</source><source>PubMed Central</source><creator>Versluis, Dennis ; de J Bello González, Teresita ; Zoetendal, Erwin G ; Passel, Mark W J van ; Smidt, Hauke</creator><contributor>Abdo, Zaid</contributor><creatorcontrib>Versluis, Dennis ; de J Bello González, Teresita ; Zoetendal, Erwin G ; Passel, Mark W J van ; Smidt, Hauke ; Abdo, Zaid</creatorcontrib><description>The emergence of bacterial pathogens that are resistant to clinical antibiotics poses an increasing risk to human health. An important reservoir from which bacterial pathogens can acquire resistance is the human gut microbiota. However, thus far, a substantial fraction of the gut microbiota remains uncultivated and has been little-studied with respect to its resistance reservoir-function. Here, we aimed to isolate yet uncultivated resistant gut bacteria by a targeted approach. Therefore, faecal samples from 20 intensive care patients who had received the prophylactic antibiotic treatment selective digestive decontamination (SDD), i.e. tobramycin, polymyxin E, amphotericin B and cefotaxime, were inoculated anaerobically on porous aluminium oxide chips placed on top of poor and rich agar media, including media supplemented with the SDD antibiotics. Biomass growing on the chips was analysed by 16S rRNA gene amplicon sequencing, showing large inter-individual differences in bacterial cultivability, and enrichment of a range of taxonomically diverse operational taxonomic units (OTUs). Furthermore, growth of Ruminococcaceae (2 OTUs), Enterobacteriaceae (6 OTUs) and Lachnospiraceae (4 OTUs) was significantly inhibited by the SDD antibiotics. Strains belonging to 16 OTUs were candidates for cultivation to pure culture as they shared ≤95% sequence identity with the closest type strain and had a relative abundance of ≥2%. Six of these OTUs were detected on media containing SDD antibiotics, and as such were prime candidates to be studied regarding antibiotic resistance. One of these six OTUs was obtained in pure culture using targeted isolation. This novel strain was resistant to the antibiotics metrodinazole and imipenem. It was initially classified as member of the Ruminococcaceae, though later it was found to share 99% nucleotide identity with the recently published Sellimonas intestinalis BR72T. In conclusion, we show that high-throughput cultivation-based screening of microbial communities can guide targeted isolation of bacteria that serve as reservoirs of antibiotic resistance.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0210970</identifier><identifier>PMID: 30653573</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Aluminum ; Aluminum Oxide ; Amphotericin B ; Anaerobiosis ; Antibiotic Prophylaxis ; Antibiotic resistance ; Antibiotics ; Antifungal agents ; Bacteria ; Bacterial infections ; Bacteriological Techniques ; Biology and Life Sciences ; Care and treatment ; Cefotaxime ; Chips ; Clostridiales - drug effects ; Clostridiales - growth & development ; Clostridiales - isolation & purification ; Cultivation ; Culture ; Culture media ; Decontamination ; Decontamination - methods ; Digestive system ; Digestive tract ; Disease Reservoirs - microbiology ; Drug resistance ; Drug Resistance, Bacterial - genetics ; Enterobacteriaceae - drug effects ; Enterobacteriaceae - genetics ; Enterobacteriaceae - isolation & purification ; Feces - microbiology ; Gastrointestinal Microbiome - drug effects ; Gastrointestinal Microbiome - genetics ; Gastrointestinal tract ; Gene sequencing ; Genes ; Health risks ; High-Throughput Screening Assays ; Humans ; Imipenem ; Intensive care ; Intensive Care Units ; Intestinal microflora ; Laboratories ; Laboratorium voor Microbiologie ; Medical screening ; Medicine and Health Sciences ; Methods ; Microbial activity ; Microbial drug resistance ; Microbial Sensitivity Tests ; Microbiological Laboratory ; Microbiologie ; Microbiology ; Microbiota ; Microbiota (Symbiotic organisms) ; Microorganisms ; MolEco ; Pathogens ; Porosity ; Public health ; Pure culture ; Relative abundance ; RNA, Bacterial - genetics ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Ruminococcaceae ; Tobramycin ; VLAG ; WIMEK</subject><ispartof>PloS one, 2019-01, Vol.14 (1), p.e0210970-e0210970</ispartof><rights>COPYRIGHT 2019 Public Library of Science</rights><rights>2019 Versluis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2019 Versluis et al 2019 Versluis et al</rights><rights>Wageningen University & Research</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c743t-a003e3e2eff073173001788d8d5077aece7ff42d270163b5f43c42f88e2572be3</citedby><cites>FETCH-LOGICAL-c743t-a003e3e2eff073173001788d8d5077aece7ff42d270163b5f43c42f88e2572be3</cites><orcidid>0000-0001-8430-4500</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2168161386/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2168161386?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,25733,27903,27904,36991,36992,44569,53769,53771,74872</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30653573$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Abdo, Zaid</contributor><creatorcontrib>Versluis, Dennis</creatorcontrib><creatorcontrib>de J Bello González, Teresita</creatorcontrib><creatorcontrib>Zoetendal, Erwin G</creatorcontrib><creatorcontrib>Passel, Mark W J van</creatorcontrib><creatorcontrib>Smidt, Hauke</creatorcontrib><title>High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The emergence of bacterial pathogens that are resistant to clinical antibiotics poses an increasing risk to human health. An important reservoir from which bacterial pathogens can acquire resistance is the human gut microbiota. However, thus far, a substantial fraction of the gut microbiota remains uncultivated and has been little-studied with respect to its resistance reservoir-function. Here, we aimed to isolate yet uncultivated resistant gut bacteria by a targeted approach. Therefore, faecal samples from 20 intensive care patients who had received the prophylactic antibiotic treatment selective digestive decontamination (SDD), i.e. tobramycin, polymyxin E, amphotericin B and cefotaxime, were inoculated anaerobically on porous aluminium oxide chips placed on top of poor and rich agar media, including media supplemented with the SDD antibiotics. Biomass growing on the chips was analysed by 16S rRNA gene amplicon sequencing, showing large inter-individual differences in bacterial cultivability, and enrichment of a range of taxonomically diverse operational taxonomic units (OTUs). Furthermore, growth of Ruminococcaceae (2 OTUs), Enterobacteriaceae (6 OTUs) and Lachnospiraceae (4 OTUs) was significantly inhibited by the SDD antibiotics. Strains belonging to 16 OTUs were candidates for cultivation to pure culture as they shared ≤95% sequence identity with the closest type strain and had a relative abundance of ≥2%. Six of these OTUs were detected on media containing SDD antibiotics, and as such were prime candidates to be studied regarding antibiotic resistance. One of these six OTUs was obtained in pure culture using targeted isolation. This novel strain was resistant to the antibiotics metrodinazole and imipenem. It was initially classified as member of the Ruminococcaceae, though later it was found to share 99% nucleotide identity with the recently published Sellimonas intestinalis BR72T. In conclusion, we show that high-throughput cultivation-based screening of microbial communities can guide targeted isolation of bacteria that serve as reservoirs of antibiotic resistance.</description><subject>Aluminum</subject><subject>Aluminum Oxide</subject><subject>Amphotericin B</subject><subject>Anaerobiosis</subject><subject>Antibiotic Prophylaxis</subject><subject>Antibiotic resistance</subject><subject>Antibiotics</subject><subject>Antifungal agents</subject><subject>Bacteria</subject><subject>Bacterial infections</subject><subject>Bacteriological Techniques</subject><subject>Biology and Life Sciences</subject><subject>Care and treatment</subject><subject>Cefotaxime</subject><subject>Chips</subject><subject>Clostridiales - drug effects</subject><subject>Clostridiales - growth & development</subject><subject>Clostridiales - isolation & purification</subject><subject>Cultivation</subject><subject>Culture</subject><subject>Culture media</subject><subject>Decontamination</subject><subject>Decontamination - methods</subject><subject>Digestive system</subject><subject>Digestive tract</subject><subject>Disease Reservoirs - microbiology</subject><subject>Drug resistance</subject><subject>Drug Resistance, Bacterial - genetics</subject><subject>Enterobacteriaceae - drug effects</subject><subject>Enterobacteriaceae - genetics</subject><subject>Enterobacteriaceae - isolation & purification</subject><subject>Feces - microbiology</subject><subject>Gastrointestinal Microbiome - drug effects</subject><subject>Gastrointestinal Microbiome - genetics</subject><subject>Gastrointestinal tract</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Health risks</subject><subject>High-Throughput Screening Assays</subject><subject>Humans</subject><subject>Imipenem</subject><subject>Intensive care</subject><subject>Intensive Care Units</subject><subject>Intestinal microflora</subject><subject>Laboratories</subject><subject>Laboratorium voor Microbiologie</subject><subject>Medical screening</subject><subject>Medicine and Health Sciences</subject><subject>Methods</subject><subject>Microbial activity</subject><subject>Microbial drug resistance</subject><subject>Microbial Sensitivity Tests</subject><subject>Microbiological Laboratory</subject><subject>Microbiologie</subject><subject>Microbiology</subject><subject>Microbiota</subject><subject>Microbiota (Symbiotic organisms)</subject><subject>Microorganisms</subject><subject>MolEco</subject><subject>Pathogens</subject><subject>Porosity</subject><subject>Public health</subject><subject>Pure culture</subject><subject>Relative abundance</subject><subject>RNA, Bacterial - genetics</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Ruminococcaceae</subject><subject>Tobramycin</subject><subject>VLAG</subject><subject>WIMEK</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNqNk89u1DAQxiMEolB4AwSWkBAcdnHsJM5yQKoqoJUqVeLf1Zo4k8SV1w6205an4JVxdrdVF_WAcnA0_s03ns-eLHuR02XORf7-wk3eglmOzuKSspyuBH2QPclXnC0qRvnDO_8H2dMQLigteV1Vj7MDTquSl4I_yf6c6H4gcfBu6odxikRNJupLiNrZRQMBWxKUR7Ta9sRZMrpEBgJmWms7rYm71i0SNehxDhp3FUgE32NMiTo4sxEiriNgo260i1oRj0GHmAJkmNZgSZ_KNqAieg3PskcdmIDPd-th9uPzp-_HJ4uz8y-nx0dnCyUKHhdAKUeODLuOCp4LTmku6rqt25IKAahQdF3BWiZoXvGm7AquCtbVNbJSsAb5YfZqqzsaF-TOyyBZXtV5lSebEnG6JVoHF3L0eg3-t3Sg5SbgfC_Bp3YMSpbKQptThLorsCigbEXRVAyBixUvZ60PW60r6DdWopUWvNJhI2h042fxq8lLa-ZlnJogy0Jskz_ujjo1a2wV2ujB7J1of8fqQfbuUlacV6wSSeDtTsC7XxOGKNc6KDQGLKbLTE2LVUGpqFlCX_-D3m_Njuohda9t51JdNYvKo7JarURdMZ6o5T1U-lpca5VebadTfC_h3V5CYiJexx6mEOTpt6__z57_3Gff3GEHBBOH9DSn-WmGfbDYgsq7EDx2tybnVM5Dd-OGnIdO7oYupb28e0G3STdTxv8C_Q8sBA</recordid><startdate>20190117</startdate><enddate>20190117</enddate><creator>Versluis, Dennis</creator><creator>de J Bello González, Teresita</creator><creator>Zoetendal, Erwin G</creator><creator>Passel, Mark W J van</creator><creator>Smidt, Hauke</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>QVL</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-8430-4500</orcidid></search><sort><creationdate>20190117</creationdate><title>High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria</title><author>Versluis, Dennis ; de J Bello González, Teresita ; Zoetendal, Erwin G ; Passel, Mark W J van ; Smidt, Hauke</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c743t-a003e3e2eff073173001788d8d5077aece7ff42d270163b5f43c42f88e2572be3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Aluminum</topic><topic>Aluminum Oxide</topic><topic>Amphotericin B</topic><topic>Anaerobiosis</topic><topic>Antibiotic Prophylaxis</topic><topic>Antibiotic resistance</topic><topic>Antibiotics</topic><topic>Antifungal agents</topic><topic>Bacteria</topic><topic>Bacterial infections</topic><topic>Bacteriological Techniques</topic><topic>Biology and Life Sciences</topic><topic>Care and treatment</topic><topic>Cefotaxime</topic><topic>Chips</topic><topic>Clostridiales - drug effects</topic><topic>Clostridiales - growth & development</topic><topic>Clostridiales - isolation & purification</topic><topic>Cultivation</topic><topic>Culture</topic><topic>Culture media</topic><topic>Decontamination</topic><topic>Decontamination - methods</topic><topic>Digestive system</topic><topic>Digestive tract</topic><topic>Disease Reservoirs - microbiology</topic><topic>Drug resistance</topic><topic>Drug Resistance, Bacterial - genetics</topic><topic>Enterobacteriaceae - drug effects</topic><topic>Enterobacteriaceae - genetics</topic><topic>Enterobacteriaceae - isolation & purification</topic><topic>Feces - microbiology</topic><topic>Gastrointestinal Microbiome - drug effects</topic><topic>Gastrointestinal Microbiome - genetics</topic><topic>Gastrointestinal tract</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Health risks</topic><topic>High-Throughput Screening Assays</topic><topic>Humans</topic><topic>Imipenem</topic><topic>Intensive care</topic><topic>Intensive Care Units</topic><topic>Intestinal microflora</topic><topic>Laboratories</topic><topic>Laboratorium voor Microbiologie</topic><topic>Medical screening</topic><topic>Medicine and Health Sciences</topic><topic>Methods</topic><topic>Microbial activity</topic><topic>Microbial drug resistance</topic><topic>Microbial Sensitivity Tests</topic><topic>Microbiological Laboratory</topic><topic>Microbiologie</topic><topic>Microbiology</topic><topic>Microbiota</topic><topic>Microbiota (Symbiotic organisms)</topic><topic>Microorganisms</topic><topic>MolEco</topic><topic>Pathogens</topic><topic>Porosity</topic><topic>Public health</topic><topic>Pure culture</topic><topic>Relative abundance</topic><topic>RNA, Bacterial - genetics</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA 16S</topic><topic>Ruminococcaceae</topic><topic>Tobramycin</topic><topic>VLAG</topic><topic>WIMEK</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Versluis, Dennis</creatorcontrib><creatorcontrib>de J Bello González, Teresita</creatorcontrib><creatorcontrib>Zoetendal, Erwin G</creatorcontrib><creatorcontrib>Passel, Mark W J van</creatorcontrib><creatorcontrib>Smidt, Hauke</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>Biological Sciences</collection><collection>Agriculture Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>ProQuest Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>ProQuest advanced technologies & aerospace journals</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>NARCIS:Publications</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Versluis, Dennis</au><au>de J Bello González, Teresita</au><au>Zoetendal, Erwin G</au><au>Passel, Mark W J van</au><au>Smidt, Hauke</au><au>Abdo, Zaid</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2019-01-17</date><risdate>2019</risdate><volume>14</volume><issue>1</issue><spage>e0210970</spage><epage>e0210970</epage><pages>e0210970-e0210970</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The emergence of bacterial pathogens that are resistant to clinical antibiotics poses an increasing risk to human health. An important reservoir from which bacterial pathogens can acquire resistance is the human gut microbiota. However, thus far, a substantial fraction of the gut microbiota remains uncultivated and has been little-studied with respect to its resistance reservoir-function. Here, we aimed to isolate yet uncultivated resistant gut bacteria by a targeted approach. Therefore, faecal samples from 20 intensive care patients who had received the prophylactic antibiotic treatment selective digestive decontamination (SDD), i.e. tobramycin, polymyxin E, amphotericin B and cefotaxime, were inoculated anaerobically on porous aluminium oxide chips placed on top of poor and rich agar media, including media supplemented with the SDD antibiotics. Biomass growing on the chips was analysed by 16S rRNA gene amplicon sequencing, showing large inter-individual differences in bacterial cultivability, and enrichment of a range of taxonomically diverse operational taxonomic units (OTUs). Furthermore, growth of Ruminococcaceae (2 OTUs), Enterobacteriaceae (6 OTUs) and Lachnospiraceae (4 OTUs) was significantly inhibited by the SDD antibiotics. Strains belonging to 16 OTUs were candidates for cultivation to pure culture as they shared ≤95% sequence identity with the closest type strain and had a relative abundance of ≥2%. Six of these OTUs were detected on media containing SDD antibiotics, and as such were prime candidates to be studied regarding antibiotic resistance. One of these six OTUs was obtained in pure culture using targeted isolation. This novel strain was resistant to the antibiotics metrodinazole and imipenem. It was initially classified as member of the Ruminococcaceae, though later it was found to share 99% nucleotide identity with the recently published Sellimonas intestinalis BR72T. In conclusion, we show that high-throughput cultivation-based screening of microbial communities can guide targeted isolation of bacteria that serve as reservoirs of antibiotic resistance.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>30653573</pmid><doi>10.1371/journal.pone.0210970</doi><tpages>e0210970</tpages><orcidid>https://orcid.org/0000-0001-8430-4500</orcidid><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1932-6203 |
ispartof | PloS one, 2019-01, Vol.14 (1), p.e0210970-e0210970 |
issn | 1932-6203 1932-6203 |
language | eng |
recordid | cdi_plos_journals_2168161386 |
source | Publicly Available Content Database; PubMed Central |
subjects | Aluminum Aluminum Oxide Amphotericin B Anaerobiosis Antibiotic Prophylaxis Antibiotic resistance Antibiotics Antifungal agents Bacteria Bacterial infections Bacteriological Techniques Biology and Life Sciences Care and treatment Cefotaxime Chips Clostridiales - drug effects Clostridiales - growth & development Clostridiales - isolation & purification Cultivation Culture Culture media Decontamination Decontamination - methods Digestive system Digestive tract Disease Reservoirs - microbiology Drug resistance Drug Resistance, Bacterial - genetics Enterobacteriaceae - drug effects Enterobacteriaceae - genetics Enterobacteriaceae - isolation & purification Feces - microbiology Gastrointestinal Microbiome - drug effects Gastrointestinal Microbiome - genetics Gastrointestinal tract Gene sequencing Genes Health risks High-Throughput Screening Assays Humans Imipenem Intensive care Intensive Care Units Intestinal microflora Laboratories Laboratorium voor Microbiologie Medical screening Medicine and Health Sciences Methods Microbial activity Microbial drug resistance Microbial Sensitivity Tests Microbiological Laboratory Microbiologie Microbiology Microbiota Microbiota (Symbiotic organisms) Microorganisms MolEco Pathogens Porosity Public health Pure culture Relative abundance RNA, Bacterial - genetics RNA, Ribosomal, 16S - genetics rRNA 16S Ruminococcaceae Tobramycin VLAG WIMEK |
title | High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria |
url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-28T04%3A27%3A58IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=High%20throughput%20cultivation-based%20screening%20on%20porous%20aluminum%20oxide%20chips%20allows%20targeted%20isolation%20of%20antibiotic%20resistant%20human%20gut%20bacteria&rft.jtitle=PloS%20one&rft.au=Versluis,%20Dennis&rft.date=2019-01-17&rft.volume=14&rft.issue=1&rft.spage=e0210970&rft.epage=e0210970&rft.pages=e0210970-e0210970&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0210970&rft_dat=%3Cgale_plos_%3EA569978623%3C/gale_plos_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c743t-a003e3e2eff073173001788d8d5077aece7ff42d270163b5f43c42f88e2572be3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2168161386&rft_id=info:pmid/30653573&rft_galeid=A569978623&rfr_iscdi=true |