{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T18:59:51Z","timestamp":1793818791220,"version":"4.6.1"},"reference-count":31,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T00:00:00Z","timestamp":1777939200000},"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. Med."],"abstract":"<jats:p>\n                    Next-generation metagenomic sequencing (mNGS) enables the direct and unbiased detection of pathogens from clinical samples, overcoming the limitations of standard methods. It is particularly valuable in immunocompromised patients and in cases of complex infections. We report the case of a man in his 40s, born in North Africa, who was admitted with progressive skin and soft-tissue lesions after a minor foot trauma. The initially localized infection rapidly worsened, leading to bilateral pneumonia, acute respiratory failure, disseminated intravascular coagulation, and death. Histopathological examination revealed granulomatous inflammation with alcohol-resistant bacilli and an undiagnosed cutaneous T-cell lymphoma associated with hemophagocytic syndrome. Conventional microbiological tests identified multiple pathogens, including influenza A virus, herpes simplex virus 1 (HSV-1),\n                    <jats:italic>Candida albicans<\/jats:italic>\n                    ,\n                    <jats:italic>Enterococcus faecalis<\/jats:italic>\n                    ,\n                    <jats:italic>Proteus mirabilis<\/jats:italic>\n                    , and\n                    <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                    ; however, their heterogeneous distribution and isolation from non-sterile sites hindered etiological interpretation. Cultures and molecular assays for\n                    <jats:italic>Mycobacterium<\/jats:italic>\n                    species were negative despite findings of histological examination suggestive of granulomatous inflammation with alcohol-resistant bacilli. To clarify the diagnosis, mNGS was performed on blood, serum, and lymph node samples using host DNA depletion and Illumina sequencing. Bioinformatic analysis revealed a diverse microbial landscape, with the detection of\n                    <jats:italic>Fusarium pseudograminearum<\/jats:italic>\n                    ,\n                    <jats:italic>Mycobacterium canettii,<\/jats:italic>\n                    and\n                    <jats:italic>Ralstonia<\/jats:italic>\n                    sp., alongside low-level viral sequences [Epstein\u2013Barr virus (\n                    <jats:italic>EBV<\/jats:italic>\n                    ) and\n                    <jats:italic>HSV-1<\/jats:italic>\n                    ]. These results reflected the patient\u2019s severe immune deficiency, characterized by a marked depletion of CD8\n                    <jats:sup>+<\/jats:sup>\n                    T cells and NK cells. Although the results became available too late to influence treatment, mNGS provided crucial diagnostic insights, demonstrating its ability to uncover hidden or rare pathogens. Early application of mNGS could significantly improve diagnostic precision and therapeutic decisions in critically ill immunocompromised patients.\n                  <\/jats:p>","DOI":"10.3389\/fmed.2026.1791094","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T04:17:17Z","timestamp":1777954637000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Case Report: Beyond conventional diagnostics: mNGS support in a complex immunocompromised patient diagnosis"],"prefix":"10.3389","volume":"13","author":[{"given":"Rossana","family":"Scutari","sequence":"first","affiliation":[{"name":"Multimodal Laboratory Research Unit, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS","place":["Rome, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeria","family":"Fox","sequence":"additional","affiliation":[{"name":"Multimodal Laboratory Research Unit, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS","place":["Rome, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martina","family":"Mastropaolo","sequence":"additional","affiliation":[{"name":"Multimodal Laboratory Research Unit, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS","place":["Rome, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Fini","sequence":"additional","affiliation":[{"name":"Microbiology and Diagnostic Immunology Unit, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS","place":["Rome, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Mussa","sequence":"additional","affiliation":[{"name":"Unit of Infectious Diseases, Department of Medical Sciences, University of Turin","place":["Turin, Italy"]},{"name":"SC Malattie Infettive, \u201cAmedeo di Savoia\u201d Hospital, ASL \u201cCitt\u00e0 di Torino\u201d","place":["Turin, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Bigliano","sequence":"additional","affiliation":[{"name":"Unit of Infectious Diseases, Department of Medical Sciences, University of Turin","place":["Turin, Italy"]},{"name":"SC Malattie Infettive, \u201cAmedeo di Savoia\u201d Hospital, ASL \u201cCitt\u00e0 di Torino\u201d","place":["Turin, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luna","family":"Colagrossi","sequence":"additional","affiliation":[{"name":"Microbiology and Diagnostic Immunology Unit, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS","place":["Rome, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gianluca","family":"Vrenna","sequence":"additional","affiliation":[{"name":"Microbiology and Diagnostic Immunology Unit, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS","place":["Rome, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Perinzano","sequence":"additional","affiliation":[{"name":"SC Malattie Infettive, \u201cAmedeo di Savoia\u201d Hospital, ASL \u201cCitt\u00e0 di Torino\u201d","place":["Turin, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Scabini","sequence":"additional","affiliation":[{"name":"Unit of Infectious Diseases, Department of Medical Sciences, University of Turin","place":["Turin, Italy"]},{"name":"Unit of Infectious Diseases, AOU Citt\u00e0 Della Salute e Della Scienza","place":["Turin, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlo Federico","family":"Perno","sequence":"additional","affiliation":[{"name":"Multimodal Laboratory Research Unit, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS","place":["Rome, Italy"]},{"name":"Microbiology and Diagnostic Immunology Unit, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS","place":["Rome, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Calcagno","sequence":"additional","affiliation":[{"name":"Department of Translational Medicine, University of Eastern Pidmont","place":["Novara, Italy"]},{"name":"SCDO Malattie Infettive, AOU Maggiore Della Carit\u00e0","place":["Novara, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,5,5]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1920","DOI":"10.1007\/s00134-024-07647-6","article-title":"Diagnostic tests for infections in critically ill immunocompromised patients","volume":"50","author":"Dumas","year":"2024","journal-title":"Intensive Care Med"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"431","DOI":"10.3201\/eid2902.221829","article-title":"Next-generation sequencing for identifying unknown pathogens in sentinel immunocompromised 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