{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:55:40Z","timestamp":1785426940109,"version":"3.56.0"},"reference-count":21,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"National institute for communicable disease control and prevention","award":["37013"],"award-info":[{"award-number":["37013"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,4,7]]},"abstract":"ABSTRACT<\/jats:title>\n \n \n \n Stenotrophomonas<\/jats:italic>\n is a significant opportunistic pathogen associated with high attributable mortality. Notably high isolation rates and species diversity have been observed among tuberculosis patients in Beijing, China. To determine its infection\/colonization rate and characteristics in non-TB patients, we conducted a study utilizing a sensitive pre-enrichment PCR assay on pharyngeal swabs from inpatients in the Department of Infectious Diseases. Three\n Stenotrophomonas<\/jats:italic>\n strains were isolated from 143 samples (2.10%), and positive cases shared common characteristics\u2014advanced age, invasive procedures, repeated hospitalizations, and broad-spectrum antimicrobial exposure\u2014which are established risk factors for\n Stenotrophomonas maltophilia<\/jats:italic>\n infection. Both the isolation rate and common characteristics differed from those of TB patients. Notably, three isolates were identified via average nucleotide identity (ANI) as\n S. geniculate<\/jats:italic>\n and\n S. muris<\/jats:italic>\n , but both species were misidentified as\n S. maltophilia<\/jats:italic>\n by matrix-assisted laser desorption\/ionization time-of-flight (MALDI-TOF) mass spectrometry, despite achieving reliable identification scores (\u22652.0). This misidentification likely explains the exclusive focus on\n S. maltophilia<\/jats:italic>\n and the underestimation of other species absent from MALDI-TOF databases. Antibiotic susceptibility testing showed general susceptibility to quinolones, tigecycline, chloramphenicol, and trimethoprim-sulfamethoxazole and partial susceptibility to ceftazidime and ceftazidime\/avibactam. Notably, a strain susceptible to ceftazidime and moxifloxacin was isolated from a patient treated with these agents. In conclusion, this study underscores the necessity of developing alternative rapid molecular methods with ANI-equivalent resolution for\n Stenotrophomonas<\/jats:italic>\n , alongside expanding mass spectral databases and reevaluating the clinical significance and resistance profiles of the\n Stenotrophomonas<\/jats:italic>\n species.\n <\/jats:p>\n \n IMPORTANCE<\/jats:title>\n \n Compounding its inherent pathogenicity,\n Stenotrophomonas<\/jats:italic>\n adversely impacts co-infecting pathogens and is associated with high attributable mortality and multidrug resistance. This study demonstrates that through enrichment and PCR of throat swab samples, this elusive pathogen\u2014frequently undetected in routine clinical testing\u2014can be identified with high sensitivity, providing crucial diagnostic alerts for clinicians, particularly in critically ill and etiology-unknown patients. Our analysis reveals that the risk factors for\n Stenotrophomonas<\/jats:italic>\n positivity differ between general infectious disease inpatients and tuberculosis patients. Furthermore, our findings highlight a critical issue of species misidentification by routine microbiological methods, which has obscured the true clinical significance and resistance profiles of\n Stenotrophomonas<\/jats:italic>\n species.\n <\/jats:p>\n <\/jats:sec>\n <\/jats:sec>","DOI":"10.1128\/spectrum.03798-25","type":"journal-article","created":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T14:21:16Z","timestamp":1772029276000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Highly effective isolation of\n Stenotrophomonas<\/i>\n from pharyngeal swabs of infected inpatients and issues in species identification"],"prefix":"10.1128","volume":"14","author":[{"given":"Boqing","family":"Xu","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04f7g6845","id-type":"ROR","asserted-by":"publisher"}],"name":"National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention","place":["Beijing, People's Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yawei","family":"Zeng","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013xs5b60","id-type":"ROR","asserted-by":"publisher"}],"name":"Beijing Friendship Hospital, Capital Medical University","place":["Beijing, People's Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-7406-6053","authenticated-orcid":true,"given":"Zelin","family":"Yu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04f7g6845","id-type":"ROR","asserted-by":"publisher"}],"name":"National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention","place":["Beijing, People's Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Jiang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04f7g6845","id-type":"ROR","asserted-by":"publisher"}],"name":"National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention","place":["Beijing, People's Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanyan","family":"Zhou","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013xs5b60","id-type":"ROR","asserted-by":"publisher"}],"name":"Beijing Friendship Hospital, Capital Medical University","place":["Beijing, People's Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Wang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013xs5b60","id-type":"ROR","asserted-by":"publisher"}],"name":"Beijing Friendship Hospital, Capital Medical University","place":["Beijing, People's Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junyi","family":"Liu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013xs5b60","id-type":"ROR","asserted-by":"publisher"}],"name":"Beijing Friendship Hospital, Capital Medical University","place":["Beijing, People's Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2258-3599","authenticated-orcid":true,"given":"Ruibai","family":"Wang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04f7g6845","id-type":"ROR","asserted-by":"publisher"}],"name":"National Key Laboratory of Intelligent 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supplement M100","author":"CLSI","year":"2023","unstructured":"CLSI. 2023. Performance standards for antimicrobial susceptibiity testing. In CLSI supplement M100, 33th ed. CLSI, Wayne, PA.","edition":"33"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00806"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2025.1629703"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1410385"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1590\/s0036-46652005000500007"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2022.09.011"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02770-24"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkae168"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03798-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03798-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T13:06:47Z","timestamp":1775567207000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.03798-25"}},"subtitle":[],"editor":[{"given":"Yanmin","family":"Wan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,4,7]]},"references-count":21,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,4,7]]}},"alternative-id":["10.1128\/spectrum.03798-25"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.03798-25","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,7]]},"assertion":[{"value":"2025-11-24","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-01-16","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-02-25","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e03798-25"}}