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Patients with malignancies represent a population at high risk for drug-resistant infections. We sought to determine the clinical spectrum and molecular epidemiology of Staphylococcus aureus infections in pediatric oncology patients followed at Texas Children’s Hospital (Houston, TX). Furthermore, we determined the prevalence of the chlorhexidine resistance gene qacA/B from isolates in this unique population.Patients with a history of malignancy and a culture-proven S. aureus infection were identified from 2001 to 2011. Antibiotic susceptibility, pulsed-field gel electrophoresis and detection of qacA/B by polymerase chain reaction were performed on all isolates. Medical records for all patients were reviewed.During the study period, 213 isolates were identified from 179 patients with malignancies. Thirty-one percent of the isolates were methicillin-resistant S. aureus. The most common infectious diagnosis was bacteremia (85/213 [39.9%], with 72/85 [84.7%] being catheter-associated). Thirteen patients with bacteremia were found to have pulmonary nodules at the time of presentation; only S. aureus was found in tissue in 5 of the 6 patients who underwent lung biopsy. After 2007, 18.2% of isolates were qacA/B positive with a steady increase in prevalence every year (χ2 for trend P = 0.04).S. aureus is a significant cause of morbidity and mortality in pediatric oncology patients at Texas Children’s Hospital. In addition to the more well-known clinical manifestations, this pathogen can also be associated with pulmonary nodules. Furthermore, the prevalence of S. aureus isolates carrying antiseptic resistance genes increased in this population. Additional clinical and molecular studies and surveillance among pediatric oncology patients are warranted to further explore these findings.