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Characteristics and etiology of infection in febrile infants aged ≤90 days. BACKGROUND: Infants ≤90 days old exhibit nonspecific signs of infection, even in cases of serious bacterial infection (SBI). METHODS: This prospective study included infants aged ≤90 days hospitalized for fever from June 2017 to August 2019. Nasopharyngeal swabs were tested using multiplex real-time PCR, and 16S ribosomal RNA analysis of whole blood was performed to determine causative microorganisms. Data pertaining to inflammatory markers, maximum body temperature (BT), and respiratory symptoms of infants and their cohabiting families were collected at admission. RESULTS: A total of 110 infants were enrolled (age range: 9-90 days), 17 (15.5%) of whom presented with SBIs. White blood cell count (WBC) and absolute neutrophil count (ANC) were significantly higher in patients with SBIs than in those without, although maximum BT did not significantly differ between the SBI and non-SBI groups (n=93). One or more viruses were detected in 82 (74.5%) infants. Viruses were detected more frequently in infants with respiratory symptoms than in those without respiratory (P=0.038), and patients with SBIs experienced significantly less respiratory symptoms than those with non-SBI (P=0.049). Moreover, viruses were more often detected in infants from cohabiting families with respiratory symptoms than in those whose family members did not exhibit respiratory symptoms (P=0.0018). CONCLUSION: WBC, and ANC were significantly higher, and experienced respiratory symptoms were less in infants ≤90 days old with SBIs than in those without. Detection of microorganisms from nasopharyngeal by multiplex real-time PCR swabs could not be judged as SBI or non-SBI.