BACKGROUND: A bacterial cause is not frequently identified in children with pneumonia complicated by parapneumonic effusion (ie, complicated pneumonia). OBJECTIVES: To determine the frequency of positive blood and pleural fluid cultures in children with complicated pneumonia and to determine whether broad‐range 16S rRNA polymerase chain reaction (PCR) improves identification of a microbiologic cause. METHODS: This prospective cohort study included children 1–18 years of age hospitalized with complicated pneumonia. RESULTS: Pleural fluid drainage was performed in 64 (51.6%) of 124 children with complicated pneumonia. A microbiologic cause was identified in 11 of 64 patients (17.2%; 95% confidence interval [CI]: 8.9%–28.7%). Bacteria were isolated from pleural fluid culture in 6 of 64 patients (9.4 %; 95% CI: 3.5%–19.3%) undergoing pleural drainage; the causative bacteria were Staphylococcus aureus (n = 5) and Streptococcus pneumoniae (n = 1). Blood culture identified a bacterial cause in 3 of 44 cases (6.8%; 95% CI: 1.4%–18.7%) undergoing pleural fluid drainage; S. pneumoniae (n = 1), Haemophilus influenzae (n = 1), and S. aureus (n = 1) were isolated. Only 3 of the 19 pleural fluid samples (15.8%; 95% CI: 3.4%–39.6%) analyzed with 16S rRNA PCR were positive. S. pneumoniae was the only organism detected in all three samples; two of these three had negative pleural fluid cultures and absence of bacteria on Gram stain. S. aureus was isolated from pleural fluid culture in one patient with a negative 16S rRNA PCR test. CONCLUSIONS: Causative bacteria were infrequently identified in children with complicated pneumonia. Broad‐range 16S rRNA PCR only modestly improved the microbiologic yield over conventional culture methods. Journal of Hospital Medicine 2011. © 2011 Society of Hospital Medicine

PARATUBERCULOSIS is a progressive wasting disease of ruminants, which is associated with chronic diarrhoea and weight loss in cattle. The disease is most economically important in cattle, sheep and goats, but Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent, has been isolated from many other ruminant and nonruminant species, including deer, rabbits and non-human primates. In human beings, MAP has been implicated in the aetiology of Crohn's disease but a definitive causal association has not been confirmed. Calves are highly susceptible to infection with MAP, while adult cattle are relatively resistant. Calves become infected within a few months of birth, but clinical signs do not become apparent until the animals are several years of age. The primary route of infection is the faecal-oral route, although the organism is excreted in the colostrum and milk of infected dams, and calves may also become infected in utero. Paratuberculosis occurs in ruminants worldwide and has a considerable economic impact. However, the effectiveness of control programmes is hampered by unreliable diagnostic tests (Nielsen and Toft 2008) and the lack of effective vaccines (Rosseels and Huygen 2008). MAP is phagocytosed by macrophages in the gastrointestinal tract but is able to resist the macrophages' intracellular killing mechanisms. It has been proposed that similar mechanisms may also allow MAP to survive for extended periods within amoebae (Rowe and Grant 2006, Whan and others 2006). Acanthamoeba polyphaga, an amoeba species commonly found in soil, can be experimentally infected with MAP (Mura and others 2006, Whan and others 2006). Previous studies have investigated the survival of MAP in the environment (Pickup and others 2005, 2006, Whittington and others 2005) and in experimentally infected amoebae, but none has directly investigated natural colonisation with MAP of free-living, environmental amoebae in soil. This study investigated the hypothesis that MAP could be identified