{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T05:56:02Z","timestamp":1792130162873,"version":"4.4.0"},"reference-count":49,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T00:00:00Z","timestamp":1781568000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010751","name":"Fondo Nacional de Desarrollo Cient\u00edfico, Tecnol\u00f3gico y de Innovaci\u00f3n Tecnol\u00f3gica","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010751","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      Aquaculture systems function as dynamic ecological interfaces facilitating the circulation of opportunistic pathogens and antimicrobial resistance (AMR) determinants across environmental, animal, and human compartments.\n                      <jats:italic>Aeromonas<\/jats:italic>\n                      spp. are ubiquitous freshwater bacteria and emerging human opportunistic pathogens, yet genomic data from tropical South American aquaculture remain scarce.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Nine\n                      <jats:italic>Aeromonas<\/jats:italic>\n                      isolates from Amazonian aquaculture facilities in Peru were subjected to whole-genome sequencing. Species identification was performed using Average Nucleotide Identity and phylogenomic reconstruction within a dataset of 112 genomes. Ribosomal MLST, comparative gene content analysis, virulence and resistome profiling, human pathogenicity prediction, and quinolone resistance-determining region (QRDR) screening were conducted. Phenotypic antimicrobial susceptibility testing was performed against five antibiotics.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Phylogenomic analysis revealed substantial genetic diversity among the analyzed isolates, encompassing\n                      <jats:italic>Aeromonas hydrophila, Aeromonas caviae<\/jats:italic>\n                      , and\n                      <jats:italic>Aeromonas veronii<\/jats:italic>\n                      , with no clustering by host species or production site. Ribosomal MLST assigned 8 distinct rSTs across the 9 isolates. Comparative genomic analysis identified 19,486 gene clusters, of which a subset was shared across all genomes, while the majority were variably distributed, indicating extensive genomic diversity across\n                      <jats:italic>Aeromonas<\/jats:italic>\n                      spp. All isolates shared conserved colonization- and secretion-associated determinants, whereas major cytotoxic toxin genes were absent. PathogenFinder v2 predicted high probabilities of human pathogenicity (0.93\u20130.96) across all genomes. Resistome analysis identified genes associated with tetracycline, quinolone, sulfonamide, and \u03b2-lactam resistance, including intrinsic blaOXA and cphA, while QRDR screening identified mutations potentially associated with quinolone resistance. Genomic findings were broadly consistent with phenotypic susceptibility profiles.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      Amazonian aquaculture systems harbor genetically diverse\n                      <jats:italic>Aeromonas<\/jats:italic>\n                      lineages with conserved opportunistic virulence traits and clinically relevant AMR determinants. These findings highlight the role of aquaculture environments as reservoirs and potential transmission interfaces of antimicrobial resistance and opportunistic pathogens, underscoring the importance of genomic surveillance within a One Health context.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1823138","type":"journal-article","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T16:10:27Z","timestamp":1781626227000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Phylogenomic and comparative genomic analyses of Aeromonas spp. from South American aquatic systems reveal extensive genomic diversity, antimicrobial resistance, and predicted human pathogenicity"],"prefix":"10.3389","volume":"17","author":[{"given":"Enrique","family":"Garcia-Candela","sequence":"first","affiliation":[{"name":"CITE productivo San Mart\u00edn, Instituto Tecnol\u00f3gico de la Producci\u00f3n","place":["San Mart\u00edn, Peru"]},{"name":"Grupo de Investigaci\u00f3n en Ciencias \u00d3micas y Bioinform\u00e1tica (GICOB), Facultad de Medicina Veterinaria, Universidad Nacional de San Mart\u00edn","place":["Tarapoto, Per\u00fa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aar\u00f3n","family":"Mondrag\u00f3n-Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Laboratorio de Biolog\u00eda Molecular y Gen\u00f3mica, Escuela profesional de Biolog\u00eda, Facultad de Ciencias Biol\u00f3gicas","place":["Universidad Ricardo Palma (URP), Peru"]},{"name":"Instituto de Calidad, Inocuidad y Seguridad Alimentaria, Universidad Ricardo Palma (URP)","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerald","family":"Moreno-Morales","sequence":"additional","affiliation":[{"name":"Unidad de Biolog\u00eda y Gen\u00e9tica Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos (UNMSM)","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milagros","family":"Cabrera-Soregui","sequence":"additional","affiliation":[{"name":"Grupo de Investigaci\u00f3n en Ciencias \u00d3micas y Bioinform\u00e1tica (GICOB), Facultad de Medicina Veterinaria, Universidad Nacional de San Mart\u00edn","place":["Tarapoto, Per\u00fa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V\u00edctor Humberto","family":"Puic\u00f3n Ni\u00f1o de Guzm\u00e1n","sequence":"additional","affiliation":[{"name":"Grupo de investigaci\u00f3n en Parasitolog\u00eda Veterinaria y Zoonosis Parasitaria, Facultad de Medicina Veterinaria, Universidad Nacional de San Mart\u00edn","place":["Tarapoto, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan C.","family":"Ramos Gorbena","sequence":"additional","affiliation":[{"name":"Instituto de Calidad, Inocuidad y Seguridad Alimentaria, Universidad Ricardo Palma (URP)","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alcides Guerra","family":"Santa Cruz","sequence":"additional","affiliation":[{"name":"Laboratorio de Biolog\u00eda Molecular y Gen\u00f3mica, Escuela profesional de Biolog\u00eda, Facultad de Ciencias Biol\u00f3gicas","place":["Universidad Ricardo Palma (URP), Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lidia","family":"Cruz-Neyra","sequence":"additional","affiliation":[{"name":"Laboratorio de Biolog\u00eda Molecular y Gen\u00f3mica, Escuela profesional de Biolog\u00eda, Facultad de Ciencias Biol\u00f3gicas","place":["Universidad Ricardo Palma (URP), Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julio","family":"Solis-Sarmiento","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00f3mica y Bioinform\u00e1tica Aplicada (Lab-Bio-Gen), Facultad de Ciencias Biol\u00f3gicas, Universidad Nacional Mayor de San Marcos (UNMSM)","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,16]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"7712","DOI":"10.1038\/s41598-023-34887-1","article-title":"Whole spectrum of Aeromonas hydrophila virulence determinants and the identification of novel SNPs using comparative pathogenomics","volume":"13","author":"Abdella","year":"2023","journal-title":"Sci. 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