High-throughput analysis of lipidomic phenotypes of methicillin-resistant Staphylococcus aureus by coupling in situ 96-well cultivation and HILIC-ion mobility-mass spectrometry
Antimicrobial resistance is a major threat to human health as resistant pathogens spread globally, and the development of new antimicrobials is slow. Since many antimicrobials function by targeting cell wall and membrane components, high-throughput lipidomics for bacterial phenotyping is of high int...
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| Veröffentlicht in: | Analytical and bioanalytical chemistry 2023-10, Vol.415 (25), p.6191-6199 |
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| creator | Zhang, Rutan Ashford, Nate K. Li, Amy Ross, Dylan H. Werth, Brian J. Xu, Libin |
| description | Antimicrobial resistance is a major threat to human health as resistant pathogens spread globally, and the development of new antimicrobials is slow. Since many antimicrobials function by targeting cell wall and membrane components, high-throughput lipidomics for bacterial phenotyping is of high interest for researchers to unveil lipid-mediated pathways when dealing with a large number of lab-selected or clinical strains. However, current practice for lipidomic analysis requires the cultivation of bacteria on a large scale, which does not replicate the growth conditions for high-throughput bioassays that are normally carried out in 96-well plates, such as susceptibility tests, growth curve measurements, and biofilm quantitation. Analysis of bacteria grown under the same condition as other bioassays would better inform the differences in susceptibility and other biological metrics. In this work, a high-throughput method for cultivation and lipidomic analysis of antimicrobial-resistant bacteria was developed for standard 96-well plates exemplified by methicillin-resistant
Staphylococcus aureus
(MRSA). By combining a 30-mm liquid chromatography (LC) column with ion mobility (IM) separation, elution time could be dramatically shortened to 3.6 min for a single LC run without losing major lipid features. Peak capacity was largely rescued by the addition of the IM dimension. Through multi-linear calibration, the deviation of retention time can be limited to within 5%, making database-based automatic lipid identification feasible. This high-throughput method was further validated by characterizing the lipidomic phenotypes of antimicrobial-resistant mutants derived from the MRSA strain, W308, grown in a 96-well plate.
Graphical abstract |
| doi_str_mv | 10.1007/s00216-023-04890-6 |
| format | Article |
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Staphylococcus aureus
(MRSA). By combining a 30-mm liquid chromatography (LC) column with ion mobility (IM) separation, elution time could be dramatically shortened to 3.6 min for a single LC run without losing major lipid features. Peak capacity was largely rescued by the addition of the IM dimension. Through multi-linear calibration, the deviation of retention time can be limited to within 5%, making database-based automatic lipid identification feasible. This high-throughput method was further validated by characterizing the lipidomic phenotypes of antimicrobial-resistant mutants derived from the MRSA strain, W308, grown in a 96-well plate.
Graphical abstract</description><identifier>ISSN: 1618-2642</identifier><identifier>EISSN: 1618-2650</identifier><identifier>DOI: 10.1007/s00216-023-04890-6</identifier><identifier>PMID: 37535099</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Analysis ; Analytical Chemistry ; Anti-Bacterial Agents - pharmacology ; Anti-Infective Agents ; Antimicrobial agents ; Antimicrobial resistance ; Bacteria ; Bioassays ; Biochemistry ; Biofilms ; Cell walls ; Characterization and Evaluation of Materials ; Chemistry ; Chemistry and Materials Science ; Column chromatography ; Cultivation ; Drug resistance ; Food Science ; Growth conditions ; Humans ; Identification and classification ; Ionic mobility ; Ions ; Laboratory Medicine ; Lipidomics ; Lipids ; Lipids - analysis ; Liquid chromatography ; Mass spectrometry ; Mass Spectrometry - methods ; Mass spectroscopy ; Methicillin ; Methicillin-Resistant Staphylococcus aureus ; Methods ; Microbial Sensitivity Tests ; Mobility ; Monitoring/Environmental Analysis ; Phenotype ; Phenotypes ; Phenotyping ; Plates ; Research Paper ; Resistant mutant ; Retention time ; Staphylococcal Infections - microbiology ; Staphylococcus aureus ; Staphylococcus infections</subject><ispartof>Analytical and bioanalytical chemistry, 2023-10, Vol.415 (25), p.6191-6199</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2023. The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.</rights><rights>COPYRIGHT 2023 Springer</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c449t-7c3ad4a49e8a97ca7187c31163d6aacfced9f7c69455de6eabd4f5e440659b983</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00216-023-04890-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00216-023-04890-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,780,784,885,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37535099$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Rutan</creatorcontrib><creatorcontrib>Ashford, Nate K.</creatorcontrib><creatorcontrib>Li, Amy</creatorcontrib><creatorcontrib>Ross, Dylan H.</creatorcontrib><creatorcontrib>Werth, Brian J.</creatorcontrib><creatorcontrib>Xu, Libin</creatorcontrib><title>High-throughput analysis of lipidomic phenotypes of methicillin-resistant Staphylococcus aureus by coupling in situ 96-well cultivation and HILIC-ion mobility-mass spectrometry</title><title>Analytical and bioanalytical chemistry</title><addtitle>Anal Bioanal Chem</addtitle><addtitle>Anal Bioanal Chem</addtitle><description>Antimicrobial resistance is a major threat to human health as resistant pathogens spread globally, and the development of new antimicrobials is slow. Since many antimicrobials function by targeting cell wall and membrane components, high-throughput lipidomics for bacterial phenotyping is of high interest for researchers to unveil lipid-mediated pathways when dealing with a large number of lab-selected or clinical strains. However, current practice for lipidomic analysis requires the cultivation of bacteria on a large scale, which does not replicate the growth conditions for high-throughput bioassays that are normally carried out in 96-well plates, such as susceptibility tests, growth curve measurements, and biofilm quantitation. Analysis of bacteria grown under the same condition as other bioassays would better inform the differences in susceptibility and other biological metrics. In this work, a high-throughput method for cultivation and lipidomic analysis of antimicrobial-resistant bacteria was developed for standard 96-well plates exemplified by methicillin-resistant
Staphylococcus aureus
(MRSA). By combining a 30-mm liquid chromatography (LC) column with ion mobility (IM) separation, elution time could be dramatically shortened to 3.6 min for a single LC run without losing major lipid features. Peak capacity was largely rescued by the addition of the IM dimension. Through multi-linear calibration, the deviation of retention time can be limited to within 5%, making database-based automatic lipid identification feasible. This high-throughput method was further validated by characterizing the lipidomic phenotypes of antimicrobial-resistant mutants derived from the MRSA strain, W308, grown in a 96-well plate.
Graphical abstract</description><subject>Analysis</subject><subject>Analytical Chemistry</subject><subject>Anti-Bacterial Agents - pharmacology</subject><subject>Anti-Infective Agents</subject><subject>Antimicrobial agents</subject><subject>Antimicrobial resistance</subject><subject>Bacteria</subject><subject>Bioassays</subject><subject>Biochemistry</subject><subject>Biofilms</subject><subject>Cell walls</subject><subject>Characterization and Evaluation of Materials</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Column chromatography</subject><subject>Cultivation</subject><subject>Drug resistance</subject><subject>Food Science</subject><subject>Growth conditions</subject><subject>Humans</subject><subject>Identification and classification</subject><subject>Ionic mobility</subject><subject>Ions</subject><subject>Laboratory Medicine</subject><subject>Lipidomics</subject><subject>Lipids</subject><subject>Lipids - analysis</subject><subject>Liquid chromatography</subject><subject>Mass spectrometry</subject><subject>Mass Spectrometry - methods</subject><subject>Mass spectroscopy</subject><subject>Methicillin</subject><subject>Methicillin-Resistant Staphylococcus aureus</subject><subject>Methods</subject><subject>Microbial Sensitivity Tests</subject><subject>Mobility</subject><subject>Monitoring/Environmental Analysis</subject><subject>Phenotype</subject><subject>Phenotypes</subject><subject>Phenotyping</subject><subject>Plates</subject><subject>Research Paper</subject><subject>Resistant mutant</subject><subject>Retention time</subject><subject>Staphylococcal Infections - microbiology</subject><subject>Staphylococcus aureus</subject><subject>Staphylococcus infections</subject><issn>1618-2642</issn><issn>1618-2650</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9UsFu1DAQjRCIloUf4IAsceHiYie2E59QVQG70kocgLPldZzElWMH22mVv-ITcbplSxFCPow9894bjecVxWuMLjBC9fuIUIkZRGUFEWk4guxJcY4ZbmDJKHp6upPyrHgR4zVCmDaYPS_OqppWFHF-Xvzcmn6AaQh-7odpTkA6aZdoIvAdsGYyrR-NAtOgnU_LpO_yo06DUcZa42DQGZykS-BrktOwWK-8UnMEcg46h8MClJ-nDO2BcSCaNAPO4K22FqjZJnMjk_Eu923BdrffXcH1NfqDsSYtcJQxgjhplYLPbcPysnjWSRv1q_u4Kb5_-vjtagv3Xz7vri73UBHCE6xVJVsiCdeN5LWSNW5yCmNWtUxK1Snd8q5WjBNKW820PLSko5oQxCg_8KbaFB-OutN8GHWrtEtBWjEFM8qwCC-NeFxxZhC9vxEYI8oxp1nh3b1C8D9mHZMYTVR5bum0n6MoG0IZJbRem739C3rt55A3saLqilU14ugB1UurhXGdz43VKioua9YgUvM836a4-Acqn1bnTXqnO5PzjwjlkaCCjzHo7jQkRmI1mjgaTWSjiTujiZX05s_vOVF-OysDqiMg5pLrdXgY6T-yvwBEyeMV</recordid><startdate>20231001</startdate><enddate>20231001</enddate><creator>Zhang, Rutan</creator><creator>Ashford, Nate K.</creator><creator>Li, Amy</creator><creator>Ross, Dylan H.</creator><creator>Werth, Brian J.</creator><creator>Xu, Libin</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><general>Springer Nature B.V</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>3V.</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7U5</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8BQ</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>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>F28</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H8D</scope><scope>H8G</scope><scope>HCIFZ</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KB.</scope><scope>KR7</scope><scope>L7M</scope><scope>LK8</scope><scope>L~C</scope><scope>L~D</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20231001</creationdate><title>High-throughput analysis of lipidomic phenotypes of methicillin-resistant Staphylococcus aureus by coupling in situ 96-well cultivation and HILIC-ion mobility-mass spectrometry</title><author>Zhang, Rutan ; Ashford, Nate K. ; Li, Amy ; Ross, Dylan H. ; Werth, Brian J. ; Xu, Libin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c449t-7c3ad4a49e8a97ca7187c31163d6aacfced9f7c69455de6eabd4f5e440659b983</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Analysis</topic><topic>Analytical Chemistry</topic><topic>Anti-Bacterial Agents - pharmacology</topic><topic>Anti-Infective Agents</topic><topic>Antimicrobial agents</topic><topic>Antimicrobial resistance</topic><topic>Bacteria</topic><topic>Bioassays</topic><topic>Biochemistry</topic><topic>Biofilms</topic><topic>Cell walls</topic><topic>Characterization and Evaluation of Materials</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Column chromatography</topic><topic>Cultivation</topic><topic>Drug resistance</topic><topic>Food Science</topic><topic>Growth conditions</topic><topic>Humans</topic><topic>Identification and classification</topic><topic>Ionic mobility</topic><topic>Ions</topic><topic>Laboratory Medicine</topic><topic>Lipidomics</topic><topic>Lipids</topic><topic>Lipids - analysis</topic><topic>Liquid chromatography</topic><topic>Mass spectrometry</topic><topic>Mass Spectrometry - methods</topic><topic>Mass spectroscopy</topic><topic>Methicillin</topic><topic>Methicillin-Resistant Staphylococcus aureus</topic><topic>Methods</topic><topic>Microbial Sensitivity Tests</topic><topic>Mobility</topic><topic>Monitoring/Environmental Analysis</topic><topic>Phenotype</topic><topic>Phenotypes</topic><topic>Phenotyping</topic><topic>Plates</topic><topic>Research Paper</topic><topic>Resistant mutant</topic><topic>Retention time</topic><topic>Staphylococcal Infections - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Analytical and bioanalytical chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Rutan</au><au>Ashford, Nate K.</au><au>Li, Amy</au><au>Ross, Dylan H.</au><au>Werth, Brian J.</au><au>Xu, Libin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>High-throughput analysis of lipidomic phenotypes of methicillin-resistant Staphylococcus aureus by coupling in situ 96-well cultivation and HILIC-ion mobility-mass spectrometry</atitle><jtitle>Analytical and bioanalytical chemistry</jtitle><stitle>Anal Bioanal Chem</stitle><addtitle>Anal Bioanal Chem</addtitle><date>2023-10-01</date><risdate>2023</risdate><volume>415</volume><issue>25</issue><spage>6191</spage><epage>6199</epage><pages>6191-6199</pages><issn>1618-2642</issn><eissn>1618-2650</eissn><abstract>Antimicrobial resistance is a major threat to human health as resistant pathogens spread globally, and the development of new antimicrobials is slow. Since many antimicrobials function by targeting cell wall and membrane components, high-throughput lipidomics for bacterial phenotyping is of high interest for researchers to unveil lipid-mediated pathways when dealing with a large number of lab-selected or clinical strains. However, current practice for lipidomic analysis requires the cultivation of bacteria on a large scale, which does not replicate the growth conditions for high-throughput bioassays that are normally carried out in 96-well plates, such as susceptibility tests, growth curve measurements, and biofilm quantitation. Analysis of bacteria grown under the same condition as other bioassays would better inform the differences in susceptibility and other biological metrics. In this work, a high-throughput method for cultivation and lipidomic analysis of antimicrobial-resistant bacteria was developed for standard 96-well plates exemplified by methicillin-resistant
Staphylococcus aureus
(MRSA). By combining a 30-mm liquid chromatography (LC) column with ion mobility (IM) separation, elution time could be dramatically shortened to 3.6 min for a single LC run without losing major lipid features. Peak capacity was largely rescued by the addition of the IM dimension. Through multi-linear calibration, the deviation of retention time can be limited to within 5%, making database-based automatic lipid identification feasible. This high-throughput method was further validated by characterizing the lipidomic phenotypes of antimicrobial-resistant mutants derived from the MRSA strain, W308, grown in a 96-well plate.
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| ispartof | Analytical and bioanalytical chemistry, 2023-10, Vol.415 (25), p.6191-6199 |
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| subjects | Analysis Analytical Chemistry Anti-Bacterial Agents - pharmacology Anti-Infective Agents Antimicrobial agents Antimicrobial resistance Bacteria Bioassays Biochemistry Biofilms Cell walls Characterization and Evaluation of Materials Chemistry Chemistry and Materials Science Column chromatography Cultivation Drug resistance Food Science Growth conditions Humans Identification and classification Ionic mobility Ions Laboratory Medicine Lipidomics Lipids Lipids - analysis Liquid chromatography Mass spectrometry Mass Spectrometry - methods Mass spectroscopy Methicillin Methicillin-Resistant Staphylococcus aureus Methods Microbial Sensitivity Tests Mobility Monitoring/Environmental Analysis Phenotype Phenotypes Phenotyping Plates Research Paper Resistant mutant Retention time Staphylococcal Infections - microbiology Staphylococcus aureus Staphylococcus infections |
| title | High-throughput analysis of lipidomic phenotypes of methicillin-resistant Staphylococcus aureus by coupling in situ 96-well cultivation and HILIC-ion mobility-mass spectrometry |
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