{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T15:51:15Z","timestamp":1789487475335,"version":"build-2803163510"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Aim<\/jats:title>\n                    <jats:p>Lower respiratory tract infections frequently involve polymicrobial disease and antimicrobial-resistant pathogens, yet conventional culture may provide an incomplete and delayed microbiological picture. This study evaluated the complementary contribution of multiplex molecular testing and conventional culture in a high-AMR cohort in Egypt.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods and results<\/jats:title>\n                    <jats:p>This retrospective cross-sectional study included 133 specimens collected at Souad Kafafi University Hospital, Egypt, during 2022\u20132023: 98 sputum records tested using the BioFire FilmArray Pneumonia Plus Panel and conventional culture with VITEK 2 susceptibility testing, and 35 blood-culture records evaluated using routine culture and BCID2 Panel. Paired molecular and culture results, descriptive analyses and multivariable logistic regression were performed. Among 133 specimen records, at least one pathogen was recorded at 58.6% (single-organism detection, 26.3%; mixed detection, 32.3%). Gram-negative bacteria predominated among organism-category detections (47.1%), followed by viruses (27.5%) and Gram-positive bacteria (25.5%). At least one AMR marker was detected in 51 records (38.3%), with blaCTX-M and blaNDM being the most frequent (each 27.8%). Among 98 paired sputum specimens, BioFire detected at least one target in 71.4%, compared with 51.0% by culture; the specimen-level PPA for any-target detection was 84.0%. Any degree of organism-level bacterial agreement was observed in 41.8%, while 58.2% showed complete discordance. Among 72 AMR-marker-positive observations with a matched cultured isolate and relevant susceptibility result, 64 demonstrated expected resistant phenotype (88.9% positive agreement). Both carbapenemases and Gram-negative detection were independently associated with phenotypic resistance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Integration of multiplex PCR and conventional culture expanded pathogen detection and provided valuable AMR profiling in resource-limited, high-resistance settings.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jambio\/lxag223","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T13:10:54Z","timestamp":1788181854000},"source":"Crossref","is-referenced-by-count":0,"title":["Complementary detection of respiratory pathogens and antimicrobial-resistance markers by multiplex PCR alongside culture in a High-AMR Egyptian cohort"],"prefix":"10.1093","volume":"137","author":[{"given":"Yasmin Adel","family":"Elmahdy","sequence":"first","affiliation":[{"name":"Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University , 11956 El Manial, Cairo ,","place":["Egypt"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atef S","family":"Elgebaly","sequence":"additional","affiliation":[{"name":"Memorial Souad Kafafi Hospital, Misr University of Science and Technology (MUST) , PO Box 77 6th of October City, Giza ,","place":["Egypt"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Menna","family":"Al-Adl","sequence":"additional","affiliation":[{"name":"Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, 35516 , Mansoura, Dakahlia ,","place":["Egypt"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heba A","family":"Elsayed","sequence":"additional","affiliation":[{"name":"Medical Microbiology and Immunology, Faculty of Medicine, Port Said University , 8541302 Al Zohour District, Port Said ,","place":["Egypt"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed E A","family":"Mostafa","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, University of Tabuk , 71491 Duba Road, Tabuk ,","place":["Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marwa M","family":"Khalifa","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Faculty of Pharmacy, Assiut University , 71526 Western District, Assiut ,","place":["Egypt"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed A","family":"Hmed","sequence":"additional","affiliation":[{"name":"Botany and Microbiology Department, Faculty of Science, Al-Azhar University , 11884 Nasr City, Cairo ,","place":["Egypt"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed R","family":"Sofy","sequence":"additional","affiliation":[{"name":"Botany and Microbiology Department, Faculty of Science, Al-Azhar 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