Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing.

Whole-genome sequencing (WGS) could potentially provide a single platform for extracting all the information required to predict an organism's phenotype. However, its ability to provide accurate predictions has not yet been demonstrated in large independent studies of specific organisms. In this study, we aimed to develop a genotypic prediction method for antimicrobial susceptibilities. The whole genomes of 501 unrelated Staphylococcus aureus isolates were sequenced, and the assembled genomes were interrogated using BLASTn for a panel of known resistance determinants (chromosomal mutations and genes carried on plasmids). Results were compared with phenotypic susceptibility testing for 12 commonly used antimicrobial agents (penicillin, methicillin, erythromycin, clindamycin, tetracycline, ciprofloxacin, vancomycin, trimethoprim, gentamicin, fusidic acid, rifampin, and mupirocin) performed by the routine clinical laboratory. We investigated discrepancies by repeat susceptibility testing and manual inspection of the sequences and used this information to optimize the resistance determinant panel and BLASTn algorithm. We then tested performance of the optimized tool in an independent validation set of 491 unrelated isolates, with phenotypic results obtained in duplicate by automated broth dilution (BD Phoenix) and disc diffusion. In the validation set, the overall sensitivity and specificity of the genomic prediction method were 0.97 (95% confidence interval [95% CI], 0.95 to 0.98) and 0.99 (95% CI, 0.99 to 1), respectively, compared to standard susceptibility testing methods. The very major error rate was 0.5%, and the major error rate was 0.7%. WGS was as sensitive and specific as routine antimicrobial susceptibility testing methods. WGS is a promising alternative to culture methods for resistance prediction in S. aureus and ultimately other major bacterial pathogens.

RED: the analysis, management and dissemination of expressed sequence tags.

The Rancourt EST Database (RED) is a web-based system for the analysis, management, and dissemination of expressed sequence tags (ESTs). RED represents a flexible template DNA sequence database that can be easily manipulated to suit the needs of other laboratories undertaking mid-size sequencing projects.

Changing the minimum legal drinking age--its effect on a central city emergency department.

AIMS: To quantify the effect of a recent national law change on the presentation of ethanol intoxicated patients to a central city Emergency Department (ED). METHODS: All records of ethanol intoxicated patients presenting to the ED for twelve months before and after the change to the minimum legal drinking age were studied. Each patient was classified as having laboratory confirmed intoxication, clinical suspicion only, or no record of intoxication. Three age groups were identified, 15-17 year olds, eighteen and nineteen year olds and over 20 year olds. Within each age group the proportion of presentations with ethanol intoxication was compared across the two time periods. RESULTS: The number of intoxicated 18 and 19 year olds increased in the twelve months after the national law change from 66 to 107 (52 to 80 for laboratory confirmed intoxication and fourteen to 27 for clinical suspicion only). This represented an increase in the proportion of presentations in this age group with intoxication (p=0.009) from 2.9% to 4.4%, a 50% increase (RR=1.51, 95%CI 1.11-2.03). There was no evidence of an increase in the proportion intoxicated for those over nineteen years (3.4% vs 3.3%, p=0.48, RR=0.97, 95%CI=0.89-1.06) although the numbers increased slightly (963 to 992). However there was a worrying trend for an increase in the 15-17 year olds, with numbers increasing from 72 to 95 and the proportion increasing from 5.0% to 6.7% (p=0.07, RR=1.35, 95%CI=0.98-1.88). CONCLUSION: The recent lowering of the minimum legal drinking age from 20 to eighteen years has resulted in increased presentations to the ED of intoxicated eighteen and nineteen year olds. A similar trend was seen in the 15-17 year olds.