{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T06:35:44Z","timestamp":1791527744863,"version":"4.3.4"},"reference-count":68,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T00:00:00Z","timestamp":1759795200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T00:00:00Z","timestamp":1759795200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100010425","name":"Tri-Service General Hospital","doi-asserted-by":"crossref","award":["TSGH-E-112216"],"award-info":[{"award-number":["TSGH-E-112216"]}],"id":[{"id":"10.13039\/501100010425","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100010425","name":"Tri-Service General Hospital","doi-asserted-by":"crossref","award":["TSGH-E-113235"],"award-info":[{"award-number":["TSGH-E-113235"]}],"id":[{"id":"10.13039\/501100010425","id-type":"DOI","asserted-by":"crossref"}]},{"name":"The Medical Affairs Bureau and National Defense Medical Center","award":["IPM-110-G2-1"],"award-info":[{"award-number":["IPM-110-G2-1"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,10,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Pneumonia imposes a significant global health burden, with high morbidity and mortality, and challenges in pathogen identification due to diverse etiologies. Conventional culture-based methods are time-consuming and insufficient for fastidious organisms, necessitating advanced diagnostic tools for rapid and accurate pathogen identification, especially in emergency department (ED) settings. To address this, we developed the pneumonia pathogen identification (PPID) assay, a multiplex diagnostic platform based on the single-stranded multiplex PCR amplicons with suspension bead array technology. The PPID assay detects 27 bacterial and viral pathogens within 6 hours. Analytical validation using nucleic acids from reference strains or synthetic oligonucleotides demonstrated high specificity and sensitivity (5\u2013500 copies per reaction). In 135 ED cases with pneumonia, the PPID assay significantly outperformed microbiological culture methods (77.8% vs 45.2%), increasing the overall detection rate to 85.9% when combined. It effectively identified polymicrobial infections in 48.6% of positive cases, including bacterial-viral co-infections, with\n                      <jats:italic toggle=\"yes\">Klebsiella pneumoniae<\/jats:italic>\n                      being the most frequently identified pathogen overall and in mixed infections. These results highlight the PPID assay\u2019s rapid and comprehensive diagnostic capability, facilitating early and targeted treatment, particularly in acute care settings. This innovative approach addresses critical unmet clinical needs and improves patient outcomes.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>\n                        <jats:bold>IMPORTANCE<\/jats:bold>\n                      <\/jats:title>\n                      <jats:p>The pneumonia pathogen identification assay is a high-throughput multiplex molecular test that detects 27 respiratory pathogens within 6 hours for up to 96 samples. It exhibits high specificity and sensitivity and enhances detection of fastidious pathogens and co-infections, addressing critical diagnostic challenges in emergency settings.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00811-25","type":"journal-article","created":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T14:54:31Z","timestamp":1756911271000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Development and diagnostic performance of a sensitive multiplex pneumonia pathogen identification assay for emergency department patients with pneumonia"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3844-127X","authenticated-orcid":true,"given":"Pei-Yi","family":"Tsui","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Graduate Institute of Medical Sciences, National Defense Medical University","place":["Taipei, Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute of Preventive Medicine, National Defense Medical University","place":["New Taipei City, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chia-Wei","family":"Hong","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical University","place":["Taipei, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Da","family":"Tsai","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical University","place":["Taipei, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chu-Yang","family":"Chien","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute of Preventive Medicine, National Defense Medical University","place":["New Taipei City, Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/00q09pe49","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Materials Science and Engineering, National Taiwan University of Science and Technology","place":["Taipe, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Ling","family":"Chen","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute of Preventive Medicine, National Defense Medical University","place":["New Taipei City, Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/00q09pe49","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Materials Science and Engineering, National Taiwan University of Science and Technology","place":["Taipe, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsin-Hsien","family":"Huang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute of Preventive Medicine, National Defense Medical University","place":["New Taipei City, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chin-Mao","family":"Hung","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Graduate Institute of Medical Sciences, National Defense Medical University","place":["Taipei, Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute of Preventive Medicine, National Defense Medical University","place":["New Taipei City, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng-Ping","family":"Lin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute of Preventive Medicine, National Defense Medical University","place":["New Taipei City, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chung-Chih","family":"Liang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute of Preventive Medicine, National Defense Medical University","place":["New Taipei City, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chih-Yuan","family":"Lin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Cardiovascular Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical University","place":["Taipei, Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"National Defense Medical University","place":["Taipei, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0215-3193","authenticated-orcid":false,"given":"Shih\u2011Hung","family":"Tsai","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical University","place":["Taipei, Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/04nx04y60","id-type":"ROR","asserted-by":"publisher"}],"name":"Taichung Armed Forces General Hospital","place":["Taichung, Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Physiology and Biophysics, Graduate Institute of Physiology, National Defense Medical University","place":["Taipei, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3895-8057","authenticated-orcid":true,"given":"Hui-Ling","family":"Hsu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Graduate Institute of Medical Sciences, National Defense Medical University","place":["Taipei, Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute of Preventive Medicine, National Defense Medical University","place":["New Taipei City, Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/02bn97g32","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, National Defense Medical University","place":["Taipei, Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanwpc.2023.100968"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph20053853"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.emc.2024.02.001"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41572-021-00259-0"},{"key":"e_1_3_4_6_2","first-page":"185","volume-title":"Encyclopedia of Respiratory Medicine","author":"Lim WS","year":"2021","unstructured":"Lim WS. 2021. Pneumonia\u2014overview, p 185\u2013197. In Encyclopedia of Respiratory Medicine"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0270261"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1055\/s-0028-1119803"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-12904-z"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2024.105307"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1080\/14787210.2019.1635010"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-020-01842-3"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/bfgp\/elr027"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics13090805"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-anchem-061622-015112"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.trac.2023.116963"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0016033"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jare.2021.09.012"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2015.06.082"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.694756"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1021\/ac400778b"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms13030662"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00055"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-34051-0"},{"key":"e_1_3_4_25_2","series-title":"Advanced Techniques in Diagnostic Microbiology","first-page":"813","volume-title":"Bead-based suspension arrays for the detection and identification of respiratory viruses","author":"Dunbar SA","year":"2012","unstructured":"Dunbar SA. 2012. Bead-based suspension arrays for the detection and identification of respiratory viruses, p 813\u2013833. Advanced Techniques in Diagnostic Microbiology. Springer."},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.3390\/jcm12206526"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10091856"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.3343\/alm.2017.37.3.267"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00517-16"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.39.2.485-493.2001"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00216-018-0931-z"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1500245"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1378\/chest.07-1456"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1136\/thx.2010.143982"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/civ1214"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.17-0249"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.21608\/mid.2021.69228.1135"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2018.01.010"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics13020280"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajic.2021.10.024"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1007\/s40121-022-00635-7"},{"key":"e_1_3_4_42_2","unstructured":"Centers Fir Disease Control ROC. 2024. Legionnaires\u2019 disease surveillance in Taiwan. Available from: https:\/\/www.cdc.gov.tw\/En\/File\/Get\/EnBINV0xwOJA9br6Fe6JzA"},{"key":"e_1_3_4_43_2","unstructured":"Centers Fir Disease Control ROC. 2025. Disease surveillance express 2024. Available from: https:\/\/www.cdc.gov.tw\/En\/File\/Get\/EnBINV0xwOJA9br6Fe6JzA. Retrieved 19 Mar 2025."},{"key":"e_1_3_4_44_2","first-page":"1370067","volume-title":"The biological mechanism and health effect of co-infection with multiple pathogens","author":"Dong L","year":"2024","unstructured":"Dong L, Xing L. 2024. The biological mechanism and health effect of co-infection with multiple pathogens, p 1370067. Frontiers Media SA."},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-46692-x"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2024.110136"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.eclinm.2021.100955"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1231740"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3005982"},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2016.11.003"},{"key":"e_1_3_4_51_2","first-page":"33","article-title":"Why is coinfection with influenza virus and bacteria so difficult to control?","volume":"19","author":"Cauley LS","year":"2015","unstructured":"Cauley LS, Vella AT. 2015. Why is coinfection with influenza virus and bacteria so difficult to control? Discov Med 19:33\u201340.","journal-title":"Discov Med"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jfma.2021.08.012"},{"key":"e_1_3_4_53_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(20)30602-2"},{"key":"e_1_3_4_54_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1508030"},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.647730"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2012.01.011"},{"key":"e_1_3_4_57_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00134-023-07108-6"},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.7759\/cureus.73298"},{"key":"e_1_3_4_59_2","doi-asserted-by":"publisher","DOI":"10.2337\/dc11-1352"},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1426200"},{"key":"e_1_3_4_61_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.903682"},{"key":"e_1_3_4_62_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00122"},{"key":"e_1_3_4_63_2","doi-asserted-by":"publisher","DOI":"10.1093\/trstmh\/tru058"},{"key":"e_1_3_4_64_2","doi-asserted-by":"publisher","DOI":"10.1515\/med-2023-0707"},{"key":"e_1_3_4_65_2","doi-asserted-by":"publisher","DOI":"10.2147\/IDR.S421587"},{"key":"e_1_3_4_66_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2021.106354"},{"key":"e_1_3_4_67_2","unstructured":"Said MS Tirthani E Lesho E. 2025. Stenotrophomonas Maltophilia. In . StatPearls."},{"key":"e_1_3_4_68_2","doi-asserted-by":"publisher","DOI":"10.1093\/jacamr\/dlac040"},{"key":"e_1_3_4_69_2","doi-asserted-by":"publisher","DOI":"10.7759\/cureus.23263"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00811-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00811-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T13:07:13Z","timestamp":1759842433000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.00811-25"}},"subtitle":[],"editor":[{"given":"Kenneth","family":"Gavina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,10,7]]},"references-count":68,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2025,10,7]]}},"alternative-id":["10.1128\/spectrum.00811-25"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.00811-25","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,7]]},"assertion":[{"value":"2025-03-22","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-06-24","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-09-03","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00811-25"}}