{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:35:09Z","timestamp":1785429309330,"version":"3.56.0"},"reference-count":64,"publisher":"American Society for Microbiology","issue":"1","license":[{"start":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T00:00:00Z","timestamp":1767657600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T00:00:00Z","timestamp":1767657600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100007000","name":"Laboratory Directed Research and Development","doi-asserted-by":"publisher","award":["17-ERD-031"],"award-info":[{"award-number":["17-ERD-031"]}],"id":[{"id":"10.13039\/100007000","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007000","name":"Laboratory Directed Research and Development","doi-asserted-by":"publisher","award":["22-SI-002"],"award-info":[{"award-number":["22-SI-002"]}],"id":[{"id":"10.13039\/100007000","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000005","name":"Department of Defense","doi-asserted-by":"publisher","award":["HU00012320037"],"award-info":[{"award-number":["HU00012320037"]}],"id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,1,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements.\n                      <jats:italic toggle=\"yes\">Acinetobacter baumannii<\/jats:italic>\n                      is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of\n                      <jats:italic toggle=\"yes\">A. baumannii<\/jats:italic>\n                      infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated \u201chigh\u201d quality. Thirty of these genomes corresponded to\n                      <jats:italic toggle=\"yes\">Acinetobacter<\/jats:italic>\n                      , with 29 mapping specifically to\n                      <jats:italic toggle=\"yes\">A. baumannii<\/jats:italic>\n                      . Other observed genera included\n                      <jats:italic toggle=\"yes\">Bordetella<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Citrobacter<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Escherichia<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">Pseudomonas<\/jats:italic>\n                      . Single-copy and multi-copy orthologs were identified across\n                      <jats:italic toggle=\"yes\">Acinetobacter<\/jats:italic>\n                      MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of\n                      <jats:italic toggle=\"yes\">de novo<\/jats:italic>\n                      metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        The ability to comprehensively and accurately characterize microbial pathogens in wound infections is critical to efficacious treatment and is especially important in the context of complex battlefield injuries. Our study shows that high-quality metagenome-assembled genomes can be obtained from shotgun metagenomic sequence data for military-relevant wound pathogens including\n                        <jats:italic toggle=\"yes\">Acinetobacter baumannii<\/jats:italic>\n                        . We demonstrate that these metagenome assemblies are directly comparable to genomes derived from cultured isolates, thereby supporting the ability to generate genome-level data sets from non-culturable biospecimens and perform comparative assessments that inform future approaches for improving diagnostic precision in military and civilian wound care.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01876-25","type":"journal-article","created":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T14:03:13Z","timestamp":1764079393000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["High-quality\n                    <i>Acinetobacter<\/i>\n                    genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7213-9392","authenticated-orcid":true,"given":"Jeffrey A.","family":"Kimbrel","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/041nk4h53","id-type":"ROR","asserted-by":"publisher"}],"name":"Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory","place":["Livermore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James B.","family":"Thissen","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/041nk4h53","id-type":"ROR","asserted-by":"publisher"}],"name":"Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory","place":["Livermore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felipe A.","family":"Lisboa","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04r3kq386","id-type":"ROR","asserted-by":"publisher"}],"name":"Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS)","place":["Bethesda, USA"]},{"name":"The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc.","place":["Bethesda, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shalini","family":"Mabery","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/041nk4h53","id-type":"ROR","asserted-by":"publisher"}],"name":"Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory","place":["Livermore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Crystal J.","family":"Jaing","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/041nk4h53","id-type":"ROR","asserted-by":"publisher"}],"name":"Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory","place":["Livermore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric A.","family":"Elster","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04r3kq386","id-type":"ROR","asserted-by":"publisher"}],"name":"Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS)","place":["Bethesda, USA"]},{"id":[{"id":"https:\/\/ror.org\/025cem651","id-type":"ROR","asserted-by":"publisher"}],"name":"Walter Reed National Military Medical Center","place":["Bethesda, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seth A.","family":"Schobel","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04r3kq386","id-type":"ROR","asserted-by":"publisher"}],"name":"Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS)","place":["Bethesda, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3478-3077","authenticated-orcid":true,"given":"Nicholas A.","family":"Be","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/041nk4h53","id-type":"ROR","asserted-by":"publisher"}],"name":"Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory","place":["Livermore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1097\/TA.0b013e318163c40b"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1097\/TA.0000000000001596"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1089\/sur.2010.110"},{"key":"e_1_3_5_5_2","unstructured":"United States Department of Defense. 2020. 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