Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray

Classical antibody-based serotyping of Escherichia coli is an important method in diagnostic microbiology for epidemiological purposes, as well as for a rough virulence assessment. However, serotyping is so tedious that its use is restricted to a few reference laboratories. To improve this situation we developed and validated a genetic approach for serotyping based on the microarray technology. The genes encoding the O-antigen flippase (wzx) and the O-antigen polymerase (wzy) were selected as target sequences for the O antigen, whereas fliC and related genes, which code for the flagellar monomer, were chosen as representatives for the H phenotype. Starting with a detailed bioinformatic analysis and oligonucleotide design, an ArrayTube-based assay was established: a fast and robust DNA extraction method was coupled with a site-specific, linear multiplex labeling procedure and hybridization analysis of the biotinylated amplicons. The microarray contained oligonucleotide DNA probes, each in duplicate, representing 24 of the epidemiologically most relevant of the over 180 known O antigens (O antigens 4, 6 to 9, 15, 26, 52, 53, 55, 79, 86, 91, 101, 103, 104, 111, 113, 114, 121, 128, 145, 157, and 172) as well as 47 of the 53 different H antigens (H antigens 1 to 12, 14 to 16, 18 to 21, 23 to 34, 37 to 43, 45, 46, 48, 49, 51 to 54, and 56). Evaluation of the microarray with a set of defined strains representing all O and H serotypes covered revealed that it has a high sensitivity and a high specificity. All of the conventionally typed 24 O groups and all of the 47 H serotypes were correctly identified. Moreover, strains which were nonmotile or nontypeable by previous serotyping assays yielded unequivocal results with the novel ArrayTube assay, which proved to be a valuable alternative to classical serotyping, allowing processing of single colonies within a single working day.

Is fast track management after elective cranial surgery safe and can it replace routine early postoperative computed tomography?

Aims: Patient management following elective cranial surgery varies between different neurosurgical institutions. Early routine postoperative cranial computed tomography (CT) is often performed while keeping patients sedated and ventilated for several hours. We hypothesize that fast track management without routine CT scanning, i.e., early extubation within one hour allowing neurological monitoring, is safe and does not increase the rate of return to OR compared with published data. Methods: We prospectively screened 1118 patients with cranial procedures performed at our department over a period of two years. 420 patients with elective brain surgery older than 18 years with no history of prior cranial surgery were included. Routine neurosurgical practice as it is performed at our department was not altered for this observational study. Fast track management was aimed for all cases, extubated and awake patients were further monitored. CT scanning within 48 hours after surgery was not performed except for unexpected neurological deterioration. This study was registered at ClinicalTrials.gov (NCT01987648). Results: 420 elective craniotomies were performed for 310 supra- and 110 infratentorial lesions. 398 patients (94.8%) were able to be extubated within 1 hour, 21 (5%) within 6 hours, and 1 patient (0.2%) was extubated 9 hours after surgery. Emergency CT within 48 hours was performed for 36 patients (8.6%, 26 supra- and 10 infratentorial cases) due to unexpected neurological worsening. Of these 36 patients 5 had to return to the OR (hemorrhage in 3, swelling in 2 cases). Return to OR rate of all included cases was 1.2%. This rate compares favorably with 1-4% as quoted in the current literature. No patient returned to the OR without prior CT imaging. Of 398 patients extubated within one hour 2 (0.5%) returned to the OR. Patients who couldn’t be extubated within the first hour had a higher risk of returning to the OR (3 of 22, i.e., 14%). Overall 30-day mortality was 0.2% (1 patient). Conclusions: Early extubation and CT imaging performed only for patients with unexpected neurological worsening after elective craniotomy procedures is safe and does not increase patient mortality or the return to OR rate. With this fast track approach early postoperative cranial CT for detection of postoperative complications in the absence of an unexpected neurological finding is not justified. Acknowledgments The authors thank Nicole Söll, study nurse, Department of Neurosurgery, Bern University Hospital, Switzerland for crucial support in data collection and managing the database.

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski's horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. Thus, they represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than nonsynonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments.