{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T18:36:55Z","timestamp":1793039815484,"version":"4.5.0"},"reference-count":72,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,7,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Methicillin-resistant\n                      <jats:italic toggle=\"yes\">Staphylococcus aureus<\/jats:italic>\n                      (MRSA) prevalence has declined in many settings, but genomic features of residual MRSA populations remain incompletely defined. We performed whole-genome sequencing (WGS) of 26\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      clinical isolates (13 MRSA and 13 methicillin-susceptible\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      [MSSA]) collected by stratified random sampling during 2024\u20132025. Analyses included\n                      <jats:italic toggle=\"yes\">de novo<\/jats:italic>\n                      assembly, species confirmation, MLST\/\n                      <jats:italic toggle=\"yes\">spa<\/jats:italic>\n                      \/SCC\n                      <jats:italic toggle=\"yes\">mec<\/jats:italic>\n                      typing, resistance and virulence profiling, mobile-element analysis, genotype\u2013phenotype concordance, and recombination-filtered\/contextual phylogenomics. A secondary matched case-control analysis explored clinical correlates. MRSA was concentrated in ST5-t895-SCC\n                      <jats:italic toggle=\"yes\">mec<\/jats:italic>\n                      II (CC5, New York\/Japan lineage; 9\/13, 69.2%), whereas MSSA was diverse (11 sequence types and 9 clonal complexes; Simpson\u2019s 1\n                      <jats:italic toggle=\"yes\">\u2212<\/jats:italic>\n                      D = 0.974 vs 0.500). SA023 (CC5-MSSA, ST5-t688) nested within the MRSA-CC5 clade and lacked SCC\n                      <jats:italic toggle=\"yes\">mec<\/jats:italic>\n                      , a pattern consistent with putative SCC\n                      <jats:italic toggle=\"yes\">mec<\/jats:italic>\n                      excision. WGS resolved lineage-specific resistance and mobile-element architectures: CC5-MRSA carried SCC\n                      <jats:italic toggle=\"yes\">mec<\/jats:italic>\n                      II with\n                      <jats:italic toggle=\"yes\">ermA<\/jats:italic>\n                      \/\n                      <jats:italic toggle=\"yes\">aadD<\/jats:italic>\n                      and quinolone resistance-determining region mutations, while SCC\n                      <jats:italic toggle=\"yes\">mec<\/jats:italic>\n                      IV MRSA belonged to CC8\/CC88 and lacked arginine catabolic mobile element\/copper and mercury resistance. Panton\u2013Valentine leukocidin genes occurred in six isolates (four community-associated MRSA and two community-associated MSSA). WGS-based resistance prediction showed 91.7% categorical agreement with phenotypes. In the exploratory clinical analysis, prior antibiotic exposure, intensive care unit admission, and healthcare exposure score were associated with MRSA. Contemporary MRSA in this hospital is clonally concentrated, while MSSA is diverse. WGS identifies lineage-specific resistance and mobile element architectures, as well as one observation consistent with SCC\n                      <jats:italic toggle=\"yes\">mec<\/jats:italic>\n                      excision, generating hypotheses for longitudinal surveillance rather than establishing a mechanism for MRSA decline. Clinical associations are secondary and exploratory.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Methicillin-resistant\n                        <jats:italic toggle=\"yes\">Staphylococcus aureus<\/jats:italic>\n                        (MRSA) infections have declined in many hospitals, but cross-sectional clinical data alone cannot explain the genomic structure of the MRSA populations that remain. This study uses whole-genome sequencing to show that contemporary MRSA isolates from a Mexican university referral hospital are concentrated in a CC5 New York\/Japan lineage, whereas methicillin-susceptible\n                        <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                        (MSSA) isolates are genetically diverse. The analysis identifies lineage-specific resistance determinants, mobile genetic elements, prophage content, defense systems, and one CC5-MSSA isolate showing a pattern consistent with SCC\n                        <jats:italic toggle=\"yes\">mec<\/jats:italic>\n                        excision. These findings provide a descriptive genomic baseline for longitudinal MRSA surveillance. The clinical risk-factor analysis is included as exploratory context, not as the primary evidence for the genomic conclusions.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00948-26","type":"journal-article","created":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T12:01:02Z","timestamp":1781524862000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Whole-genome sequencing of\n                    <i>Staphylococcus aureus<\/i>\n                    isolates after a decade-long decline in MRSA prevalence at a university referral hospital in Guadalajara, Mexico: clonal concentration in MRSA and greater genetic diversity in MSSA"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1948-655X","authenticated-orcid":false,"given":"Jaime F.","family":"Andrade-Villanueva","sequence":"first","affiliation":[{"name":"Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara","place":["Guadalajara, Mexico"]},{"name":"Antiguo Hospital Civil de Guadalajara \u201cFray Antonio Alcalde\u201d","place":["Guadalajara, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0505-6340","authenticated-orcid":false,"given":"Pedro","family":"Mart\u00ednez-Ayala","sequence":"additional","affiliation":[{"name":"Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara","place":["Guadalajara, Mexico"]},{"name":"Antiguo Hospital Civil de Guadalajara \u201cFray Antonio Alcalde\u201d","place":["Guadalajara, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adolfo","family":"Gomez-Quiroz","sequence":"additional","affiliation":[{"name":"Antiguo Hospital Civil de Guadalajara \u201cFray Antonio Alcalde\u201d","place":["Guadalajara, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3767-6867","authenticated-orcid":false,"given":"Violeta Cassandra","family":"Vera-Cuevas","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas del Noroeste, S. C.","place":["La Paz, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0251-6425","authenticated-orcid":false,"given":"Judith Carolina","family":"De Arcos-Jim\u00e9nez","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/000sg7415","id-type":"ROR","asserted-by":"publisher"}],"name":"Centro Universitario de Tlajomulco, Universidad de Guadalajara","place":["Tlajomulco de Z\u00fa\u00f1iga, Mexico"]},{"name":"Hospital Civil de Oriente","place":["Tonal\u00e1, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1901-392X","authenticated-orcid":true,"given":"Jaime","family":"Briseno-Ramirez","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/000sg7415","id-type":"ROR","asserted-by":"publisher"}],"name":"Centro Universitario de Tlajomulco, Universidad de Guadalajara","place":["Tlajomulco de Z\u00fa\u00f1iga, Mexico"]},{"name":"Hospital Civil de Oriente","place":["Tonal\u00e1, Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.mm6809e1"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM199808203390806"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00134-14"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-018-0147-4"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(21)02724-0"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1001\/jamainternmed.2013.10423"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1086\/676534"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1017\/ice.2023.102"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02168-21"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/cmr.00148-22"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01239-06"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.40.11.4289-4294.2002"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkw570"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01520-09"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.969961"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofy270"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx350"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-020-01881-w"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0317284"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiv320"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1081070"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics15030242"},{"key":"e_1_3_5_24_2","series-title":"CLSI Document M100","volume-title":"Performance standards for antimicrobial susceptibility testing","author":"Clinical and Laboratory Standards Institute","year":"2024","unstructured":"Clinical and Laboratory Standards Institute. 2024. 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