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Culture-based agglutination has been the gold standard for serotyping, but it is limited by logistics, subjectivity, and the availability of antisera for emerging serotypes. Newer methods, including a real-time PCR-based approach and whole-genome sequencing offer alternatives, but their performance in\n                      <jats:italic>Shigella<\/jats:italic>\n                      endemic populations are not well documented.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Shigella<\/jats:italic>\n                      isolates obtained from the Enterics for Global Health (EFGH) study in Iquitos, Peru were simultaneously serotyped using four methods: culture-based agglutination, isolate-based real-time PCR serotyping, stool-based real-time PCR serotyping and WGS using the in-silico tool ShigaPass. The definitive adjudicated serotype was established by an expert analysis of the WGS data, involving the mapping of sequence reads to known O-antigen biosynthesis and modification genes to identify key mutations.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Results from all four serotyping methods were available for 107\/114 isolates. Accuracy for vaccine subtypes\n                      <jats:italic>S. flexneri<\/jats:italic>\n                      1b, 2a, 3a, 6, and\n                      <jats:italic>S. sonnei<\/jats:italic>\n                      , ranged from 93.3-100% for all methods. Complete concordance between methods was noted in 83\/107 isolates, while 24\/107 (22.4%) exhibited at least one discrepancy. Most discrepancies derived from\n                      <jats:italic>S. flexneri<\/jats:italic>\n                      serotypes Y, Yv and 1a. Agglutination misclassified eight Y\/Yv isolates as 4a, and six isolates correctly classified as 1a by agglutination were classified as 1b by the other methods, a discrepancy associated with a nonsense mutation in the\n                      <jats:italic>oac<\/jats:italic>\n                      gene.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      All four serotyping methods achieved acceptable accuracy for\n                      <jats:italic>Shigella<\/jats:italic>\n                      vaccine efficacy evaluation. Although discrepancies are infrequent, WGS provides information of their genomic basis.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pntd.0014668","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T17:54:11Z","timestamp":1787766851000},"page":"e0014668","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Robust performance of culture, real-time PCR, and genomic approaches for shigella serotyping in a pediatric surveillance cohort"],"prefix":"10.1371","volume":"20","author":[{"given":"Francesca","family":"Schiaffino","sequence":"first","affiliation":[{"name":"Universidad Peruana Cayetano Heredia","place":["San Martin de Porres, Lima, Peru"],"department":["Faculty of Veterinary Medicine"]},{"name":"School of Medicine, University of Virginia","place":["Charlottesville, Virginia, United States of America"],"department":["Division 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