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Acute conjunctivitis is the most common eye disorder in young children. Bacteria are responsible for 54–73% of all cases. The goals of the study were to identify the rates of Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis in cases of bacterial conjunctivitis in children and to define antibiotic resistance rates.During a 2-year study period, conjunctival swabs of children 2–36 months old were collected prospectively. Nontypable H. influenzae, S. pneumoniae and M. catarrhalis were defined as the study pathogens. Analyzed variables included demography, clinical presentation, bacteriologic results and susceptibility patterns.There were 428 patients enrolled. Of all cultures, 55% (237 of 428) yielded at least 1 of the study pathogens. H. influenzae and S. pneumoniae were isolated from 29 and 20% of cultures, respectively. β-Lactamase production was found in 29% of H. influenzae isolates, and penicillin nonsusceptibility was observed in 60% of S. pneumoniae isolates. The most common S. pneumoniae serotypes were: 19F (14%); 6A and 14 (11% each). Nontypable S. pneumoniae was found in 12%. The 7-valent pneumococcal conjugate vaccine (PCV-7) could potentially cover 44% of all isolates. Conjunctivitis-otitis syndrome was found in 32% of patients, of whom 82% of cultures yielded H. influenzae.Antibiotic resistance rates are alarmingly high. Conjunctivitis-otitis syndrome, predominantly caused by H. influenzae, is quite common. The potential coverage of the PCV-7 in conjunctivitis is relatively lower than that reported in other pneumococcal infections. Our findings should alert physicians on the choice of appropriate antibiotic treatment, on the frequent copresence of acute otitis media and on the potential role of conjunctivitis in the spread of antibiotic-resistant pathogens.