Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K. pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for K. pneumoniae based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of K. pneumoniae into three distinct species, KpI (K. pneumoniae), KpII (K. quasipneumoniae), and KpIII (K. variicola). Further, for K. pneumoniae (KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show K. pneumoniae has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive K. pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats.

Dr. C. J. Verfaillie's affiliations were incomplete. They have been amended to include her former affiliation in Rotterdam where the study took place and should read as follows:

Introduction Streptococcus pneumoniae is a worldwide occurring pathogen Nasopharyngeal carriage of Streptococcus pneumoniae precedes pneumonia and other pneumococcal diseases in the community. Little is known about S. pneumoniae carriage in Indonesia, complicating strategies to control pneumococcal diseases. We investigated nasopharyngeal carriage of S. pneumoniae in Semarang, Indonesia.MethodsA population-based survey was performed in Semarang, Indonesia. Nasopharyngeal swabs and questionnaires were taken from 496 healthy young (6–60 month-old) children and 45–70 year-old adults.ResultsForty-three percent of children aged 6–60 months and 11% of adults aged 45–75 years carried S. pneumoniae. Determinants of carriage were being a child (OR 7.7; 95% CI = 4.5–13.0), passive smoking (OR 2.1; 95% CI = 1.3–3.4), and contact with toddler(s) at home (OR 3.0; 95% CI = 1.9–4.7). The most frequent serotypes found were 6A/B and 15B/C. The current commercially available vaccines cover <50% serotypes found in children. Twenty-four percent of S. pneumoniae strains were penicillin non-susceptible, and 45% were resistant to cotrimoxazol.ConclusionsThe limited coverage of commercially available vaccines against the serotypes found in this population, and the high proportion of non-susceptibility to penicillin and cotrimoxazol suggest the need for region-specific information and strategies to control S. pneumoniae.

A systematic review and meta-analyses were performed to identify the risk factors associated with carbapenem-resistant Pseudomonas aeruginosa and to identify sources and reservoirs for the pathogen. A systematic search of PubMed and Embase databases from 1 January 1987 until 27 January 2012 identified 1,662 articles, 53 of which were included in a systematic review and 38 in a random-effects meta-analysis study. The use of carbapenem, use of fluoroquinolones, use of vancomycin, use of other antibiotics, having medical devices, intensive care unit (ICU) admission, having underlying diseases, patient characteristics, and length of hospital stay were significant risk factors in multivariate analyses. The meta-analyses showed that carbapenem use (odds ratio [OR] ‫؍‬ 7.09; 95% confidence interval [CI] ‫؍‬ 5.43 to 9.25) and medical devices (OR ‫؍‬ 5.11; 95% CI ‫؍‬ 3.55 to 7.37) generated the highest pooled estimates. Cumulative meta-analyses showed that the pooled estimate of carbapenem use was stable and that the pooled estimate of the risk factor "having medical devices" increased with time. We conclude that our results highlight the importance of antibiotic stewardship and the thoughtful use of medical devices in helping prevent outbreaks of carbapenem-resistant P. aeruginosa.

BackgroundHand hygiene is recognized as an important measure to prevent healthcare-associated infections. Hand hygiene adherence among healthcare workers is associated with their knowledge and perception. This study aimed to evaluate the effect of three different educational programs on improving hand hygiene compliance, knowledge, and perception among healthcare workers in a tertiary care hospital in Indonesia.MethodsThe study was performed from May to October 2014 and divided into a pre-intervention, intervention, and post-intervention phase. This cluster randomized controlled trial allocated the implementation of three interventions to the departments, including role model training-pediatrics, active presentation-surgery, a combination of role model training and active presentation-internal medicine, and a control group-obstetrics-gynecology. Both direct observation and knowledge-perception survey of hand hygiene were performed using WHO tools.ResultsHand hygiene compliance was observed during 2,766 hand hygiene opportunities, and knowledge-perception was assessed among 196 participants in the pre-intervention and 88 in the post-intervention period. After intervention, the hand hygiene compliance rate improved significantly in pediatrics (24.1% to 43.7%; P < 0.001), internal medicine (5.2% to 18.5%; P < 0.001), and obstetrics-gynecology (10.1% to 20.5%; P < 0.001). The nurses’ incorrect use of hand rub while wearing gloves increased as well (P < 0.001). The average knowledge score improved from 5.6 (SD = 2.1) to 6.2 (SD = 1.9) (P < 0.05). In the perception survey, “strong smell of hand alcohol” as a reason for non-compliance increased significantly in the departments with intervention (10.1% to 22.9%; P = 0.021).ConclusionThe educational programs improved the hand hygiene compliance and knowledge among healthcare workers in two out of three intervention departments in a limited-resource hospital in Indonesia. Role model training had the most impact in this setting. However, adjustments to the strategy are necessary to further improve hand hygiene.