The rapid identification of antimicrobial resistance is essential for effective treatment of highly resistant Mycobacterium tuberculosis. Whole-genome sequencing provides comprehensive data on resistance mutations and strain typing for monitoring transmission, but unlike for conventional molecular tests, this has previously been achievable only from cultures of M. tuberculosis. Here we describe a method utilizing biotinylated RNA baits designed specifically for M. tuberculosis DNA to capture full M. tuberculosis genomes directly from infected sputum samples, allowing whole-genome sequencing without the requirement of culture. This was carried out on 24 smear-positive sputum samples, collected from the United Kingdom and Lithuania where a matched culture sample was available, and 2 samples that had failed to grow in culture. M. tuberculosis sequencing data were obtained directly from all 24 smear-positive culture-positive sputa, of which 20 were of high quality (>20؋ depth and >90% of the genome covered). Results were compared with those of conventional molecular and culture-based methods, and high levels of concordance between phenotypical resistance and predicted resistance based on genotype were observed. High-quality sequence data were obtained from one smear-positive culture-negative case. This study demonstrated for the first time the successful and accurate sequencing of M. tuberculosis genomes directly from uncultured sputa. Identification of known resistance mutations within a week of sample receipt offers the prospect for personalized rather than empirical treatment of drug-resistant tuberculosis, including the use of antimicrobial-sparing regimens, leading to improved outcomes.T he global incidence of multidrug-resistant (MDR), extensively drug-resistant (XDR), and totally drug-resistant tuberculosis (TB) has risen over the last decade (1), making it increasingly important to rapidly and accurately detect resistance. The gold standard for antimicrobial resistance testing relies on bacterial culture, which can take upwards of several weeks for Mycobacterium tuberculosis. Molecular tests, such as the Xpert (MTB/RIF) and line probe assays, which can be used directly on sputum have improved identification of MDR M. tuberculosis but are able to identify only limited numbers of specific resistance mutations (2, 3).Whole-genome sequencing (WGS) of bacterial genomes allows simultaneous identification of all known resistance mutations as well as markers with which transmission can be monitored (4). WGS of M. tuberculosis provides resolution superior to that of other current methods such as spoligotyping and mycobacterial interspersed repetitive-unit-variable-number tandemrepeat (MIRU-VNTR) analysis for strain genotyping (5), and its usefulness in defining outbreaks has been demonstrated previously (6-9). Currently, however, WGS of M. tuberculosis requires prior bacterial enrichment by culturing and most outbreak studies have therefore been retrospective (6-8). Recently, WGS of M. tuberculosis has been achieved ...

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Staphylococcus aureus is the most common cause of hospital-acquired bacteremia. From 1995 through 2000, data on age, sex, patient specialty at time of first bacteremia, primary and secondary sites of infection, delay in initiating antimicrobial therapy, and patient outcome were prospectively recorded for 815 patients with nosocomial S. aureus bacteremia. The proportion of patients whose death was attributable to methicillin-resistant S. aureus (MRSA) was significantly higher than that for methicillin-susceptible S. aureus (MSSA) (11.8% vs. 5.1%; odds ratio [OR], 2.49; 95% confidence interval [CI], 1.46-4.24; P<.001). After adjustment for host variables, the OR decreased to 1.72 (95% CI, 0.92-3.20; P=.09). There was no significant difference between rates of disseminated infection (7.1% vs. 6.2% for MRSA-infected patients and MSSA-infected patients, respectively; P=.63), though the rate of death due to disseminated infection was significantly higher than death due to uncomplicated infection (37% vs. 10% for MRSA-infected patients [P<.001] and 37% vs. 3% for MSSA-infected patients [P<.001]). There was a strong statistical trend toward death due to nosocomial MRSA infection and bacteremia, compared with MSSA.

The proportion of bacteraemias caused by biliary tract infection was 5.5%. The most common infecting organisms were E coli and K pneumoniae. There was a strong association with choledocholithiasis and malignancies, both pre-existing and newly diagnosed. Death was uncommon but when it occurred was often caused by septic shock within 48 h of presentation.