{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T07:07:12Z","timestamp":1790838432993,"version":"4.1.0"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,5,31]],"date-time":"2017-05-31T00:00:00Z","timestamp":1496188800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,5,31]],"date-time":"2017-05-31T00:00:00Z","timestamp":1496188800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Carbapenemase producing organisms (CPOs) represent an urgent public health threat, and the need for new rapid methods to detect these organisms has been widely recognized. CPOs carrying the <jats:italic>Klebsiella pneumoniae<\/jats:italic> carbapenemase (<jats:italic>bla<\/jats:italic><jats:sub>\n                  <jats:italic>KPC<\/jats:italic>\n                <\/jats:sub>) gene have caused outbreaks globally with substantial attributable mortality. Here we describe the validation of a rapid MS method for the direct detection of unique tryptic peptides of the KPC protein in clinical bacterial isolates with an isolate-to-result time of less than 90\u2009minutes. Using a genoproteomic discovery approach that combines theoretical peptidome analysis and liquid chromatography-tandem MS (LC-MS\/MS), we selected three high abundance peptide markers of the KPC protein that can be robustly detected following rapid tryptic digestion. Protein BLAST analysis confirmed that the chosen peptide markers were unique to KPC. A blinded validation set containing 20 KPC-positive and 80 KPC-negative clinical isolates, performed in triplicate (300 runs) demonstrated 100% sensitivity and 100% specificity (60\/60 positive identifications, 240\/240 negative identifications) using defined rules for positive calls. The most robust tryptic peptide marker in the validation was LTLGSALAAPQR. The peptide discovery and detection methods validated here are general and should be broadly applicable to allow the direct and rapid detection of other resistance determinants.<\/jats:p>","DOI":"10.1038\/s41598-017-02749-2","type":"journal-article","created":{"date-parts":[[2017,5,24]],"date-time":"2017-05-24T10:20:40Z","timestamp":1495621240000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Peptide Markers for Rapid Detection of KPC Carbapenemase by LC-MS\/MS"],"prefix":"10.1038","volume":"7","author":[{"given":"Honghui","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven K.","family":"Drake","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jung-Ho","family":"Youn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Avi Z.","family":"Rosenberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marjan","family":"Gucek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony F.","family":"Suffredini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John P.","family":"Dekker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,5,31]]},"reference":[{"key":"2749_CR1","unstructured":"Centers for Disease Control. Antibiotic Resistance Threats in the United States. http:\/\/www.cdc.gov\/drugresistance\/threat-report-2013\/ (2013)."},{"key":"2749_CR2","unstructured":"World Health Organization. Antimicrobial Resistance: Global Report on Surveillance http:\/\/www.who.int\/drugresistance\/documents\/surveillancereport\/en\/ (2014)."},{"key":"2749_CR3","doi-asserted-by":"publisher","first-page":"148ra116","DOI":"10.1126\/scitranslmed.3004129","volume":"4","author":"ES Snitkin","year":"2012","unstructured":"Snitkin, E. S. et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med \n                           4, 148ra116, doi:10.1126\/scitranslmed.3004129 (2012).","journal-title":"Sci Transl Med"},{"key":"2749_CR4","doi-asserted-by":"publisher","first-page":"254ra126","DOI":"10.1126\/scitranslmed.3009845","volume":"6","author":"S Conlan","year":"2014","unstructured":"Conlan, S. et al. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med \n                           6, 254ra126, doi:10.1126\/scitranslmed.3009845 (2014).","journal-title":"Sci Transl Med"},{"key":"2749_CR5","doi-asserted-by":"publisher","unstructured":"Jayol, A., Poirel, L., Dortet, L. & Nordmann, P. National survey of colistin resistance among carbapenemase-producing Enterobacteriaceae and outbreak caused by colistin-resistant OXA-48-producing Klebsiella pneumoniae, France, 2014. Euro Surveill \n                           21, doi:10.2807\/1560-7917.ES.2016.21.37.30339 (2016).","DOI":"10.2807\/1560-7917.ES.2016.21.37.30339"},{"key":"2749_CR6","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1111\/1469-0691.12719","volume":"20","author":"P Nordmann","year":"2014","unstructured":"Nordmann, P. & Poirel, L. The difficult-to-control spread of carbapenemase producers among Enterobacteriaceae worldwide. Clin Microbiol Infect \n                           20, 821\u2013830, doi:10.1111\/1469-0691.12719 (2014).","journal-title":"Clin Microbiol Infect"},{"key":"2749_CR7","doi-asserted-by":"publisher","first-page":"4490","DOI":"10.1128\/AAC.00107-16","volume":"60","author":"KM Kazmierczak","year":"2016","unstructured":"Kazmierczak, K. M. et al. Global Dissemination of blaKPC into Bacterial Species beyond Klebsiella pneumoniae and In Vitro Susceptibility to Ceftazidime-Avibactam and Aztreonam-Avibactam. Antimicrob Agents Chemother \n                           60, 4490\u20134500, doi:10.1128\/AAC.00107-16 (2016).","journal-title":"Antimicrob Agents Chemother"},{"key":"2749_CR8","doi-asserted-by":"publisher","first-page":"4073","DOI":"10.1128\/AAC.00452-16","volume":"60","author":"KD Chavda","year":"2016","unstructured":"Chavda, K. D., Chen, L., Jacobs, M. R., Bonomo, R. A. & Kreiswirth, B. N. Molecular Diversity and Plasmid Analysis of KPC-Producing Escherichia coli. Antimicrob Agents Chemother \n                           60, 4073\u20134081, doi:10.1128\/AAC.00452-16 (2016).","journal-title":"Antimicrob Agents Chemother"},{"key":"2749_CR9","doi-asserted-by":"publisher","unstructured":"van Duin, D. & Doi, Y. The global epidemiology of carbapenemase-producing Enterobacteriaceae. Virulence, 1\u201310, doi:10.1080\/21505594.2016.1222343 (2016).","DOI":"10.1080\/21505594.2016.1222343"},{"key":"2749_CR10","unstructured":"White House National Action Plan for Combating Antibiotic-Resistant Bacteria. https:\/\/www.whitehouse.gov\/sites\/default\/files\/docs\/national_action_plan_for_combating_antibotic-resistant_bacteria.pdf. (2015)."},{"key":"2749_CR11","doi-asserted-by":"publisher","first-page":"2856","DOI":"10.1093\/jac\/dkw208","volume":"71","author":"CG Monteferrante","year":"2016","unstructured":"Monteferrante, C. G. et al. Evaluation of different pretreatment protocols to detect accurately clinical carbapenemase-producing Enterobacteriaceae by MALDI-TOF. J Antimicrob Chemother \n                           71, 2856\u20132867, doi:10.1093\/jac\/dkw208 (2016).","journal-title":"J Antimicrob Chemother"},{"key":"2749_CR12","doi-asserted-by":"publisher","first-page":"1896","DOI":"10.1128\/JCM.00749-16","volume":"54","author":"AC Ramos","year":"2016","unstructured":"Ramos, A. C. et al. Influence of Culture Media on Detection of Carbapenem Hydrolysis by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol \n                           54, 1896\u20131898, doi:10.1128\/JCM.00749-16 (2016).","journal-title":"J Clin Microbiol"},{"key":"2749_CR13","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s12941-016-0120-x","volume":"15","author":"B Ghebremedhin","year":"2016","unstructured":"Ghebremedhin, B., Halstenbach, A., Smiljanic, M., Kaase, M. & Ahmad-Nejad, P. MALDI-TOF MS based carbapenemase detection from culture isolates and from positive blood culture vials. Ann Clin Microbiol Antimicrob \n                           15, 5, doi:10.1186\/s12941-016-0120-x (2016).","journal-title":"Ann Clin Microbiol Antimicrob"},{"key":"2749_CR14","doi-asserted-by":"publisher","first-page":"2225","DOI":"10.1007\/s10096-015-2473-z","volume":"34","author":"C Mirande","year":"2015","unstructured":"Mirande, C. et al. Rapid detection of carbapenemase activity: benefits and weaknesses of MALDI-TOF MS. Eur J Clin Microbiol Infect Dis \n                           34, 2225\u20132234, doi:10.1007\/s10096-015-2473-z (2015).","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"2749_CR15","doi-asserted-by":"publisher","first-page":"2163","DOI":"10.1128\/JCM.03467-14","volume":"53","author":"C Lasserre","year":"2015","unstructured":"Lasserre, C. et al. Efficient Detection of Carbapenemase Activity in Enterobacteriaceae by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Less Than 30 Minutes. J Clin Microbiol \n                           53, 2163\u20132171, doi:10.1128\/JCM.03467-14 (2015).","journal-title":"J Clin Microbiol"},{"key":"2749_CR16","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.mimet.2014.07.004","volume":"105","author":"M Sauget","year":"2014","unstructured":"Sauget, M., Cabrolier, N., Manzoni, M., Bertrand, X. & Hocquet, D. Rapid, sensitive and specific detection of OXA-48-like-producing Enterobacteriaceae by matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry. J Microbiol Methods \n                           105, 88\u201391, doi:10.1016\/j.mimet.2014.07.004 (2014).","journal-title":"J Microbiol Methods"},{"key":"2749_CR17","doi-asserted-by":"publisher","first-page":"147","DOI":"10.4155\/bio.12.310","volume":"5","author":"DR Peaper","year":"2013","unstructured":"Peaper, D. R. et al. Rapid detection of carbapenemase activity through monitoring ertapenem hydrolysis in Enterobacteriaceae with LC-MS\/MS. Bioanalysis \n                           5, 147\u2013157, doi:10.4155\/bio.12.310 (2013).","journal-title":"Bioanalysis"},{"key":"2749_CR18","doi-asserted-by":"publisher","first-page":"2441","DOI":"10.1128\/JCM.01002-12","volume":"50","author":"J Hrabak","year":"2012","unstructured":"Hrabak, J. et al. Detection of NDM-1, VIM-1, KPC, OXA-48, and OXA-162 carbapenemases by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol \n                           50, 2441\u20132443, doi:10.1128\/JCM.01002-12 (2012).","journal-title":"J Clin Microbiol"},{"key":"2749_CR19","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.mimet.2016.10.005","volume":"131","author":"CA Huber","year":"2016","unstructured":"Huber, C. A. et al. Detection of carbapenemase activity in Enterobacteriaceae using LC-MS\/MS in comparison with the neo-rapid CARB kit using direct visual assessment and colorimetry. J Microbiol Methods \n                           131, 68\u201372, doi:10.1016\/j.mimet.2016.10.005 (2016).","journal-title":"J Microbiol Methods"},{"key":"2749_CR20","doi-asserted-by":"publisher","first-page":"2500","DOI":"10.1128\/JCM.00547-14","volume":"52","author":"MV Kulkarni","year":"2014","unstructured":"Kulkarni, M. V. et al. Use of imipenem to detect KPC, NDM, OXA, IMP, and VIM carbapenemase activity from gram-negative rods in 75 minutes using liquid chromatography-tandem mass spectrometry. J Clin Microbiol \n                           52, 2500\u20132505, doi:10.1128\/JCM.00547-14 (2014).","journal-title":"J Clin Microbiol"},{"key":"2749_CR21","first-page":"571","volume":"38","author":"C Foschi","year":"2015","unstructured":"Foschi, C. et al. Use of liquid chromatography-tandem mass spectrometry (LC-MS\/MS) to detect carbapenemase production in Enterobacteriaceae by a rapid meropenem degradation assay. New Microbiol \n                           38, 571\u2013576 (2015).","journal-title":"New Microbiol"},{"key":"2749_CR22","doi-asserted-by":"publisher","first-page":"2804","DOI":"10.1128\/JCM.00694-14","volume":"52","author":"AF Lau","year":"2014","unstructured":"Lau, A. F. et al. A rapid matrix-assisted laser desorption ionization-time of flight mass spectrometry-based method for single-plasmid tracking in an outbreak of carbapenem-resistant Enterobacteriaceae. J Clin Microbiol \n                           52, 2804\u20132812, doi:10.1128\/JCM.00694-14 (2014).","journal-title":"J Clin Microbiol"},{"key":"2749_CR23","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1128\/JCM.01643-15","volume":"54","author":"JH Youn","year":"2016","unstructured":"Youn, J. H. et al. Clinical Performance of a Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Method for Detection of Certain blaKPC-Containing Plasmids. J Clin Microbiol \n                           54, 35\u201342, doi:10.1128\/JCM.01643-15 (2016).","journal-title":"J Clin Microbiol"},{"key":"2749_CR24","unstructured":"Charretier, Y. et al. Method of detecting at least one mechanism of resistance to carbapenems by mass spectrometry. Patent US 20150031063 (2012)."},{"key":"2749_CR25","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1002\/prca.201600041","volume":"10","author":"Y Charretier","year":"2016","unstructured":"Charretier, Y. & Schrenzel, J. Mass spectrometry methods for predicting antibiotic resistance. Proteomics Clin Appl \n                           10, 964\u2013981, doi:10.1002\/prca.201600041 (2016).","journal-title":"Proteomics Clin Appl"},{"key":"2749_CR26","doi-asserted-by":"publisher","first-page":"2802","DOI":"10.1021\/ac303326a","volume":"85","author":"CJ Chang","year":"2013","unstructured":"Chang, C. J. et al. Diagnosis of beta-lactam resistance in Acinetobacter baumannii using shotgun proteomics and LC-nano-electrospray ionization ion trap mass spectrometry. Anal Chem \n                           85, 2802\u20132808, doi:10.1021\/ac303326a (2013).","journal-title":"Anal Chem"},{"key":"2749_CR27","doi-asserted-by":"publisher","first-page":"9154","DOI":"10.1021\/ac502049p","volume":"86","author":"F Fleurbaaij","year":"2014","unstructured":"Fleurbaaij, F. et al. Capillary-electrophoresis mass spectrometry for the detection of carbapenemases in (multi-)drug-resistant Gram-negative bacteria. Anal Chem \n                           86, 9154\u20139161, doi:10.1021\/ac502049p (2014).","journal-title":"Anal Chem"},{"key":"2749_CR28","doi-asserted-by":"publisher","first-page":"13944","DOI":"10.1038\/srep13944","volume":"5","author":"Y Charretier","year":"2015","unstructured":"Charretier, Y. et al. Rapid Bacterial Identification, Resistance, Virulence and Type Profiling using Selected Reaction Monitoring Mass Spectrometry. Sci Rep \n                           5, 13944, doi:10.1038\/srep13944 (2015).","journal-title":"Sci Rep"},{"key":"2749_CR29","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1373\/clinchem.2015.253468","volume":"62","author":"H Wang","year":"2016","unstructured":"Wang, H. et al. A Novel Peptidomic Approach to Strain Typing of Clinical Acinetobacter baumannii Isolates Using Mass Spectrometry. Clin Chem \n                           62, 866\u2013875, doi:10.1373\/clinchem.2015.253468 (2016).","journal-title":"Clin Chem"},{"key":"2749_CR30","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1038\/nbt.1524","volume":"27","author":"VA Fusaro","year":"2009","unstructured":"Fusaro, V. A., Mani, D. R., Mesirov, J. P. & Carr, S. A. Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol \n                           27, 190\u2013198, doi:10.1038\/nbt.1524 (2009).","journal-title":"Nat Biotechnol"},{"key":"2749_CR31","doi-asserted-by":"publisher","first-page":"5145","DOI":"10.1021\/pr300273g","volume":"11","author":"T Glatter","year":"2012","unstructured":"Glatter, T. et al. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C\/trypsin proteolysis over trypsin digestion. J Proteome Res \n                           11, 5145\u20135156, doi:10.1021\/pr300273g (2012).","journal-title":"J Proteome Res"},{"key":"2749_CR32","doi-asserted-by":"publisher","first-page":"5533","DOI":"10.1016\/j.jprot.2012.07.043","volume":"75","author":"M Damm","year":"2012","unstructured":"Damm, M. et al. Can electromagnetic fields influence the structure and enzymatic digest of proteins? A critical evaluation of microwave-assisted proteomics protocols. J Proteomics \n                           75, 5533\u20135543, doi:10.1016\/j.jprot.2012.07.043 (2012).","journal-title":"J Proteomics"},{"key":"2749_CR33","doi-asserted-by":"publisher","first-page":"910","DOI":"10.1021\/pr300955f","volume":"12","author":"JS Kim","year":"2013","unstructured":"Kim, J. S., Monroe, M. E., Camp, D. G. 2nd, Smith, R. D. & Qian, W. J. In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics. J Proteome Res \n                           12, 910\u2013916, doi:10.1021\/pr300955f (2013).","journal-title":"J Proteome Res"},{"key":"2749_CR34","unstructured":"Centers for Disease Control. Multiplex Real-Time PCR Detection of Klebsiella pneumoniae Carbapenemase (KPC) and New Delhi metallo-beta-lactamase (NDM-1) https:\/\/www.cdc.gov\/HAI\/pdfs\/labSettings\/KPC-NDM-protocol-2011.pdf (2011)."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-02749-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-02749-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-02749-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T04:41:49Z","timestamp":1671770509000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-02749-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,5,31]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["2749"],"URL":"https:\/\/doi.org\/10.1038\/s41598-017-02749-2","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,5,31]]},"assertion":[{"value":"14 December 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 April 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 May 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"2531"}}