{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T05:52:24Z","timestamp":1785909144222,"version":"3.56.0"},"reference-count":51,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:00:00Z","timestamp":1785888000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"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                      Carbapenem non-susceptible\n                      <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                      is a major global health threat driven by the spread of high-risk lineages, but the genomic architecture of resistance evolution is often unresolved by short-read sequencing.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Here, we used long-read whole-genome sequencing to characterize 20 clinical\n                      <jats:italic>P. aeruginosa<\/jats:italic>\n                      isolates collected sporadically during routine clinical care as part of the ERACE-PA surveillance programme from a single tertiary hospital in Cape Town, South Africa, between December 2015 and March 2016.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Of these isolates, 18 (90%) were resistant or intermediate resistant to imipenem and\/or meropenem. Resistance determinants, mobile genetic elements, and virulence factors were strongly lineage structured. In the high-risk ST233 lineage, resistance was marked by extensive duplication of antimicrobial resistance genes across non-contiguous chromosomal loci. Genes including\n                      <jats:italic>dfrB5<\/jats:italic>\n                      ,\n                      <jats:italic>floR2<\/jats:italic>\n                      ,\n                      <jats:italic>tet(G)<\/jats:italic>\n                      ,\n                      <jats:italic>arr-5<\/jats:italic>\n                      , and\n                      <jats:italic>sul1<\/jats:italic>\n                      occurred in up to three copies (\n                      <jats:italic>sul1<\/jats:italic>\n                      ) or two copies (\n                      <jats:italic>dfrB5<\/jats:italic>\n                      ,\n                      <jats:italic>floR2<\/jats:italic>\n                      ,\n                      <jats:italic>tet(G)<\/jats:italic>\n                      ,\n                      <jats:italic>arr-5<\/jats:italic>\n                      ) across all seven ST233 isolates, distributed on distinct genomic islands, revealing a dispersed amplification architecture that is invisible to short-read approaches because repetitive IS elements and integron boundaries flanking each copy preclude unambiguous mapping and phase-resolved assembly. These loci were linked by shared insertion sequences, class 1 integrons, and transposon-associated segments, consistent with modular transposition and co-integration driving intrachromosomal spread. In contrast, ST273 showed a more plasmid-associated resistance strategy, whereas ST235 displayed more limited duplication despite carrying related mobile resistance modules. Virulence repertoires also differed by lineage: ST233 and ST260 were predominantly ExoS positive, whereas ST273 was ExoU positive.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      Together, these findings show that carbapenem non-susceptible in South African\n                      <jats:italic>P. aeruginosa<\/jats:italic>\n                      is shaped not only by gene acquisition but also by genomic structural redistribution and duplication across separate chromosomal sites, highlighting the value of long-read genomics for resolving genomic structural resistance mechanisms in\n                      <jats:italic>P. aeruginosa<\/jats:italic>\n                      surveillance.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1891542","type":"journal-article","created":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T05:39:34Z","timestamp":1785908374000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["High-resolution long-read sequencing maps genomic Island\u2013associated gene duplication in South African carbapenem non-susceptible Pseudomonas aeruginosa"],"prefix":"10.3389","volume":"17","author":[{"given":"Rory","family":"Cave","sequence":"first","affiliation":[{"name":"Centre for Innovation in Genomics and Microbiome Sciences, School of Medicine and Biosciences, University of West London","place":["London, United Kingdom"]},{"name":"Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London","place":["London, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fadheela","family":"Patel","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, University of Cape Town","place":["Cape Town, South Africa"]},{"name":"Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology","place":["Bellville, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha D.","family":"Africa","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, University of Cape Town","place":["Cape Town, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clinton","family":"Moodley","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, University of Cape Town","place":["Cape Town, South Africa"]},{"name":"National Health Laboratory Service Laboratory, Groote Schuur Hospital","place":["Cape Town, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gert","family":"Marais","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, University of Cape Town","place":["Cape Town, South Africa"]},{"name":"Crick Africa Network, Francis Crick Institute","place":["London, United Kingdom"]},{"name":"Centre for Infectious Diseases Research in Africa, University of Cape Town","place":["Cape Town, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Widaad","family":"Zemanay","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, University of Cape Town","place":["Cape Town, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian","family":"Brink","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, University of Cape Town","place":["Cape Town, South Africa"]},{"name":"National Health Laboratory Service Laboratory, Groote Schuur Hospital","place":["Cape Town, South Africa"]},{"name":"Institute of Infectious Disease and Molecular Medicine, University of Cape Town","place":["Cape Town, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hermine V.","family":"Mkrtchyan","sequence":"additional","affiliation":[{"name":"Centre for Innovation in Genomics and Microbiome Sciences, School of Medicine and Biosciences, University of West London","place":["London, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"e0172882","DOI":"10.1371\/journal.pone.0172882","article-title":"Identification of extensive drug resistant Pseudomonas aeruginosa strains: New clone ST1725 and high-risk clone ST233.","volume":"12","author":"Aguilar-Rodea","year":"2017","journal-title":"PLoS One"},{"key":"B2","doi-asserted-by":"publisher","first-page":"e00991","DOI":"10.1128\/aem.00991-22","article-title":"mobileOG-db: A manually curated database of protein families mediating the life cycle of bacterial mobile genetic elements.","volume":"88","author":"Brown","year":"2022","journal-title":"Appl. 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