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<p>Abstract</p> <p>Background</p> <p>There is increasing evidence that community acquired <it>S. aureus </it>infections are spreading among healthy children. Nasal colonization with <it>S. aureus </it>plays pivotal role in the increasing prevalence of resistant community acquired <it>S. aureus </it>infections worldwide. A regular surveillance system is important in ensuring quality of patient care. The aim of the study was to assess the prevalence of and the factors associated with nasal carriage of <it>S. aureus </it>and its antibiotic sensitivity pattern among healthy children in Ujjain, India.</p> <p>Methods</p> <p>A prospective study was done in paediatric outpatient clinics of R.D. Gardi medical college Ujjain, India. Healthy children from 1 month to 59 months of age were included. Information on previously known risk factors for nasal colonization was collected using a pre-tested questionnaire. Swabs from anterior nares were collected and transported in Amies transport media with charcoal and cultured on 5% sheep blood agar. Antibiotic sensitivity tests were performed using Kirby Bauer's disc diffusion method according to performance standards of Clinical and Laboratory Standard Institute guidelines.</p> <p>Results</p> <p>Of the 1,562 children from 1-month up-to five years of age included in the study 98 children tested positive for nasal carriage of <it>S. aureus</it>. The prevalence of nasal carriage of <it>S. aureus </it>was 6.3% (95% CI 5.1-7.5) out of which 16.3% (95% CI 8.9-23.8) were methicillin-resistant <it>S. aureus </it>(MRSA). The factors associated with nasal carriage were "child attending preschool" (OR 4.26, 95% CI 2.25-8.03; <it>P </it>= 0.007) or "school" (OR 3.02, 95% CI 1.27-7.18; <it>P </it>< 0.001) and "family size more than 10 members" (OR 2.76 95% CI 1.06-7.15; <it>P </it>= 0.03). The sensitivity pattern of isolated <it>S. aureus </it>showed resistance to commonly used oral antibiotics while resistance to glycopeptides was not noted.</p> <p>Conclusions</p> <p>We found a relatively low rate of nasal carriage of <it>S. aureus </it>in children below five years when compared to children of older age groups in India. Yet, prevalence of MRSA was relatively high.</p>