{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T00:08:06Z","timestamp":1791418086377,"version":"4.3.3"},"reference-count":17,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2020,5,1]],"date-time":"2020-05-01T00:00:00Z","timestamp":1588291200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,5,1]],"date-time":"2020-05-01T00:00:00Z","timestamp":1588291200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Clinical Laboratory Analysis"],"published-print":{"date-parts":[[2020,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Aim<\/jats:title>\n                    <jats:p>Here, we evaluated the performance of two commercial MALDI\u2010TOF MS systems and three biochemical\u2010based systems and compared them to WGS as the gold standard for identifying isolates of vancomycin\u2010resistant enterococci (VRE).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A total of 87 VRE clinical isolates were included. The mass spectrometers were the Microflex system with Biotyper software 3.1 and the Vitek MS system. The biochemical\u2010based systems included the Vitek 2, Phoenix, and MicroScan WalkAway systems. WGS was performed on an Illumina MiSeq instrument using the MiSeq v3 reagent kit. Vancomycin resistance was determined according to CLSI criteria.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Among the 87 VRE, 71 and 16 were identified as\n                      <jats:italic>Enterococcus faecium<\/jats:italic>\n                      and\n                      <jats:italic>Enterococcus faecalis<\/jats:italic>\n                      by WGS. All 71\n                      <jats:italic>E\u00a0faecium<\/jats:italic>\n                      were correctly identified by both mass spectrometers, as well as the Vitek 2 and Phoenix instruments. However, only 51\n                      <jats:italic>E\u00a0faecium<\/jats:italic>\n                      isolates were correctly identified by the MicroScan system. The most frequent misidentification was\n                      <jats:italic>Enterococcus\u00a0casseliflavus<\/jats:italic>\n                      (n\u00a0=\u00a020). For vancomycin\u2010resistant\n                      <jats:italic>E\u00a0faecium<\/jats:italic>\n                      , the Microflex Biotyper system had the highest sensitivity (85.54%), and all instruments (except for the Microscan) had a 100% specificity and PPV. Up to 87% of\n                      <jats:italic>E\u00a0faecalis<\/jats:italic>\n                      isolates were misidentified by VITEK MS and VITEK2, 81% by Microscan and Phoenix, and 75% by Bruker biotyper.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>As the coverage of type strain\u2010genome sequence database continues to grow and the cost of DNA sequencing continues to decrease, genome\u2010based identification can be a useful tool for diagnostic laboratories, with its superior accuracy even over MALDI\u2010TOF and database\u2010driven operations.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/jcla.23348","type":"journal-article","created":{"date-parts":[[2020,5,2]],"date-time":"2020-05-02T01:29:42Z","timestamp":1588382982000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Species identification of\n                    <i>Enterococcus<\/i>\n                    spp: Whole genome sequencing compared to three biochemical test\u2010based systems and two Matrix\u2010Assisted Laser Desorption\/Ionization Time\u2010of\u2010Flight Mass Spectrometry (MALDI\u2010TOF MS) systems"],"prefix":"10.1002","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5831-9661","authenticated-orcid":false,"given":"Elvira","family":"Garza\u2010Gonz\u00e1lez","sequence":"first","affiliation":[{"name":"Hospital Universitario \u201cDr. Jos\u00e9 Eleuterio Gonz\u00e1lez\u201d Universidad Aut\u00f3noma de Nuevo Le\u00f3n Monterrey Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paola","family":"Bocanegra\u2010Ibarias","sequence":"additional","affiliation":[{"name":"Hospital Universitario \u201cDr. Jos\u00e9 Eleuterio Gonz\u00e1lez\u201d Universidad Aut\u00f3noma de Nuevo Le\u00f3n Monterrey Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"An","family":"Dinh","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics (CARMiG) McGovern Medical School UTHealth Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rayo","family":"Morf\u00edn\u2010Otero","sequence":"additional","affiliation":[{"name":"Centro Universitario de Ciencias de la Salud Hospital Civil de Guadalajara \u201cFray Antonio Alcalde\u201d e Instituto de Patolog\u00eda Infecciosa y Experimental Universidad de Guadalajara Guadalajara Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adri\u00e1n","family":"Camacho\u2010Ortiz","sequence":"additional","affiliation":[{"name":"Hospital Universitario \u201cDr. Jos\u00e9 Eleuterio Gonz\u00e1lez\u201d Universidad Aut\u00f3noma de Nuevo Le\u00f3n Monterrey Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1744-9173","authenticated-orcid":false,"given":"Fabi\u00e1n","family":"Rojas\u2010Larios","sequence":"additional","affiliation":[{"name":"Facultad de Medicina Universidad de Colima Colima Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia","family":"Rodr\u00edguez\u2010Zulueta","sequence":"additional","affiliation":[{"name":"Hospital General Dr. Manuel Gea Gonz\u00e1lez Mexico City Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cesar A.","family":"Arias","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics (CARMiG) McGovern Medical School UTHealth Houston TX USA"},{"name":"School of Public Health Center for Infectious Diseases UTHealth Houston TX USA"},{"name":"Molecular Genetics and Antimicrobial Resistance Unit and International Center for Microbial Genomics Universidad El Bosque Bogot\u00e1 Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2020,5,1]]},"reference":[{"key":"e_1_2_7_2_1","volume-title":"Manual of Clinical Microbiology","author":"Pr M","year":"2011"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01859-16"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1590\/0037-8682-0123-2013"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01725-14"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.21775\/cimb.023.017"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1111\/ijcp.13332"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1086\/600885"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2011.00298.x"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.03385-14"},{"key":"e_1_2_7_11_1","volume-title":"M100\u2013S26. 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