The purpose of this study was to evaluate the clinical utility of bacterial rRNA-targeted reverse transcription-quantitative PCR (BrRNA RT-qPCR) assays for identifying the bacterial pathogens that cause fever with neutropenia in pediatric cancer patients, by comparing the bacterial detection rate of this technique with that of blood culture. One milliliter of blood was collected from pediatric patients who developed fever with neutropenia following cancer chemotherapy. BrRNA RT-qPCR was performed using 16 primer sets, each designed for a specific type of bacteria. The entire BrRNA RT-qPCR procedure took less than 5 h. Blood culture was performed at the same time, following the standard institutional procedure. Blood from 13 patients was collected during 23 febrile neutropenic episodes. Of these samples, bacteria were identified in 16 by BrRNA RT-qPCR (69.6%) and in 4 by blood culture (17.4%, P < 0.001). In all 4 blood culture-positive samples, BrRNA RT-qPCR detected the same type of bacteria as that identified by culture. In 9 samples, more than 4 types of bacteria were identified simultaneously by BrRNA RT-qPCR, most of which were anaerobic bacteria known to be part of the gut flora. We conclude that BrRNA RT-qPCR could be useful in the diagnosis of fever with neutropenia, given its high bacterial detection rate, short turnaround time, and the small blood sample required compared with the standard blood culture techniques. Our findings also indicate that anaerobic intestinal bacteria, which are difficult to detect by standard culture techniques, may be responsible for some cases of febrile neutropenia.Fever with neutropenia is a frequent complication in patients undergoing cancer chemotherapy. Because bacterial infection is considered to be the most common cause of this complication, which can be life threatening if untreated, it is recommended that antibiotic treatment be started immediately when neutropenic patients develop fever (10, 17, 18). However, blood culture, a current standard microbiological assessment for febrile neutropenic patients, can identify pathogens in only 10 to 37% of these patients (4,6,7,19) and can take more than 24 h to yield a report. Therefore, the majority of cases are treated empirically with broad-spectrum antibiotics and without microbiological evidence to support the treatment. More sensitive techniques would help physicians optimize the therapy for individual cases of fever with neutropenia.We recently developed a technique, bacterial rRNA-targeted reverse transcription-quantitative PCR (BrRNA RTqPCR), to detect subdominant bacterial populations in feces (12,13,23). In an in vitro study, we also showed that BrRNA RT-qPCR can be used to detect bacteria in blood samples (12), but we did not seek to identify bacterial pathogens in a clinical setting.The objective of this study was to evaluate the clinical utility of BrRNA RT-qPCR for identifying the bacterial pathogens responsible for fever in neutropenic patients. We conducted BrRNA RT-qPCR on blood samples from pediatric cancer...

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