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.

A pilot programme to evaluate Indonesia’s antimicrobial resistance containment plan shows that progress is on the right track, but substantial strengthening is needed, say Harry Parathon and colleagues

Physicians from these different three countries had very different attitudes on spirituality, religiosity, and health. Ethnicity and culture can have an important influence on how spirituality is approached in medical practice. S/R curricula that train physicians how to address spirituality in clinical practice must take these differences into account.

The prevalence of antimicrobial resistance among the commensal microflora was examined in the Indonesian population inside and outside hospitals. A total of 3,995 individuals were screened in two major urban centers. Among Escherichia coli from rectal samples (n = 3,284) the prevalence of resistance to ciprofloxacin and other classes of antibiotics was remarkably high, especially in individuals at the time of discharge from hospital. Staphylococcus aureus isolates (n = 361) were often resistant to tetracycline (24.9%), but this was not associated with hospital stay. Two S. aureus isolates harbored the mecA gene. Regional differences in resistance rates exist, suggesting regional differences in selection pressure, i.e., antibiotic usage patterns. The results show that antimicrobial resistance among commensal E. coli and S. aureus has emerged in Indonesia.