{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T17:52:17Z","timestamp":1787161937230,"version":"build-2736575974"},"reference-count":70,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T00:00:00Z","timestamp":1777939200000},"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":[[2026,5,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Shotgun metagenomics, when sufficient read depth exists for each taxon, enables capturing metagenome-assembled genomes (MAGs) directly from a microbial community. In 2021, an aromatherapy spray contaminated with\n                      <jats:italic toggle=\"yes\">Burkholderia pseudomallei<\/jats:italic>\n                      caused an outbreak of melioidosis in the United States. Metagenome-assembled genome binning depends in part on different nucleotide compositions, and the contaminated aromatherapy spray contained other bacteria, including related species (e.g.,\n                      <jats:italic toggle=\"yes\">Burkholderia cepacia<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Burkholderia cenocepacia<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Burkholderia multivorans<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Burkholderia pseudomultivorans<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Cupriavidus pauculus<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">Pseudomonas aeruginosa<\/jats:italic>\n                      with average nucleotide identity (ANI) to\n                      <jats:italic toggle=\"yes\">B. pseudomallei<\/jats:italic>\n                      being 84.2%, 84.4%, 84.7%, 84.8%, 75.7%, and 72.3%, respectively, and AAI being 79.5%, 79.8%, 80.5%, 80.4%, 62.5%, and 52.9%, respectively). We performed metagenomic sequencing on the contaminated aromatherapy spray to determine if a public metagenomic pipeline (\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/nf-core\/mag\" xlink:type=\"simple\">https:\/\/github.com\/nf-core\/mag<\/jats:ext-link>\n                      ) can form a MAG of\n                      <jats:italic toggle=\"yes\">B. pseudomallei<\/jats:italic>\n                      . Upon completion of the pipeline, inter- and intracontig comparisons revealed few potential contaminants of related taxa. Conservative removal of those contigs was especially valuable, ultimately obtaining an ANI of 99.9% between the\n                      <jats:italic toggle=\"yes\">B. pseudomallei<\/jats:italic>\n                      MAG and the genome of an isolate from the aromatherapy spray. This underscores the importance of quality checking recovered MAGs (e.g., for congeneric chimerism) for high-resolution objectives such as outbreak pathogenomics. Importantly, our analysis revealed that the identical conclusion was made possible with the\n                      <jats:italic toggle=\"yes\">B. pseudomallei<\/jats:italic>\n                      MAG (as with its corresponding isolate genome), which was that the aromatherapy\n                      <jats:italic toggle=\"yes\">B. pseudomallei<\/jats:italic>\n                      originated from South Asia (specifically India). Because rapid read-based (k-mer) taxonomic classification methods often report false positives, this operational framework could be valuable for rapid biothreat radar detection systems in public health surveillance.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        In 2021, an imported aromatherapy spray caused a U.S. outbreak of melioidosis after contamination with\n                        <jats:italic toggle=\"yes\">Burkholderia pseudomallei<\/jats:italic>\n                        . Using shotgun metagenomics, we reconstructed a near-complete genome of the pathogen directly from the product, despite the presence of other related microbes. The assembled genome showed 99.9% similarity to a cultured isolate. This work demonstrates that metagenomics can recover high-quality pathogen genomes from complex samples, supporting outbreak investigations and enhancing public health surveillance.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.02926-25","type":"journal-article","created":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T13:00:37Z","timestamp":1774875637000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agent\n                    <i>Burkholderia pseudomallei<\/i>\n                    for rapid public health response events"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9580-3089","authenticated-orcid":true,"given":"Gregory 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