Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the "Beijing" sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive.

Microbiological tined-lead examination: does prolonged sacral neuromodulation testing induce infection?

OBJECTIVE: To investigate whether prolonged sacral neuromodulation (SNM) testing induces a substantial risk of infection because of the percutaneous passage of the extension wire. PATIENTS AND METHODS: A consecutive series of 20 patients with negative prolonged SNM testing for >or=14 days who underwent tined-lead explantation were prospectively evaluated. The explanted tined leads were sent for microbiological examination. The tined lead, gluteal, and extension wire incision sites were investigated for clinical signs of infection according to the Centers for Disease Control and Prevention classification system. RESULTS: In all, 17 patients had bilateral and three unilateral implanted tined leads. The median (range) test period was 30 (21-62 days). Bacterial growth (Staphylococcus species) was detected in four of 20 (20%) patients on seven of 37 (19%) explanted tined leads. There were clinical signs of infection in one of 20 (5%) patients at none of 37 tined lead, one of 20 (5%) gluteal, and none of 20 extension wire incision sites. There were no clinical signs of infection in the remaining three of four patients with bacterial growth. CONCLUSIONS: After prolonged tined-lead testing, we found an infection rate comparable to that reported with the usual short test period. In addition, most patients with bacterial growth on tined leads showed no clinical signs of infection. Thus, prolonged tined-lead testing does not seem to induce clinically relevant infection, warranting randomized trials.

Impact of surgical training on incidence of surgical site infection

BACKGROUND: Despite availability of other training forms, tutorial assistance cannot be entirely replaced in surgical education. Concerns exist that tutorial assistance may lead to an increased rate of surgical site infection (SSI). The purpose of the present study was to investigate whether the risk of SSI is higher after surgery with tutorial assistance than after surgery performed autonomously by a fully trained surgeon. METHODS: All consecutive visceral, vascular, and traumatological inpatient procedures at a Swiss University Hospital were prospectively recorded during a 24-month period, and the patients were followed for 12 months to ascertain the occurrence of SSI. Using univariable and multivariable logistic regressions, we assessed the association of tutorial assistance surgery with SSI in 6,103 interventions. RESULTS: Autonomously performed surgery was associated with SSI in univariable analysis (5.36% SSI vs. 3.81% for tutorial assistance, p = 0.006). In multivariable analysis, the odds of SSI for tutorial assistance was no longer significantly lower (Odds Ratio [OR] = 0.82; 95% Confidence Interval [CI]: 0.62-1.09; p = 0.163). CONCLUSIONS: Surgical training does not lead to higher SSI rate if trainees are adequately supervised and interventions are carefully selected. Although other forms of training are useful, tutorial assistance in the operating room continues to be the mainstay of surgical education.

Phylogeny of Pasteurellaceae

This chapter provides an overview on the DNA based phylogeny of the family Pasteurellaceae and the genetic relatedness between taxa taking into account the various gene targets and approaches applied in the literature. The classical 16S rRNA gene based phylogeny as well as phylogenies based on house-keeping genes are described. Moreover, strength and weakness of the different trees and their topology are discussed based on the phylogenetic groups resolved. The data should help to get a clearer picture on the recent, current and future classification and also provide information to genetic characterization of members of the family. The history of phylogeny applied to the family as well as the phylogenetic history of the family is thereby presented. In this way it is the story of the search for the optimal phylogenetic marker without giving a final conclusive suggestion but it is also a resource for choosing the appropriate gene target(s) for people investigating the phylogeny of groups of Pasteurellaceae.

Endoscopically assisted nerve decompression of rare nerve compression syndromes at the upper extremity

BACKGROUND Besides carpal tunnel and cubital tunnel syndrome, other nerve compression or constriction syndromes exist at the upper extremity. This study was performed to evaluate and summarize our initial experience with endoscopically assisted decompression. MATERIALS AND METHODS Between January 2011 and March 2012, six patients were endoscopically operated for rare compression or hour-glass-like constriction syndrome. This included eight decompressions: four proximal radial nerve decompressions, and two combined proximal median nerve and anterior interosseus nerve decompressions. Surgical technique and functional outcomes are presented. RESULTS There were no intraoperative complications in the series. Endoscopy allowed both identifying and removing all the compressive structures. In one case, the proximal radial neuropathy developed for 10 years without therapy and a massive hour-glass nerve constriction was observed intraoperatively which led us to perform a concurrent complementary tendon transfer to improve fingers and thumb extension. Excellent results were achieved according to the modified Roles and Maudsley classification in five out of six cases. All but one patient considered the results excellent. The poorest responder developed a CRPS II and refused post-operative physiotherapy. CONCLUSION Endoscopically assisted decompression in rare compression syndrome of the upper extremity is highly appreciated by patients and provides excellent functional results. This minimally invasive surgical technique will likely be further described in future clinical studies.

The effect of idursulfase on growth in patients with Hunter syndrome: data from the Hunter Outcome Survey (HOS)

Hunter syndrome (mucopolysaccharidosis type II) is a rare and life-limiting multisystemic disorder with an X-linked recessive pattern of inheritance. Short stature is a prominent feature of this condition. This analysis aimed to investigate the effects of enzyme replacement therapy with idursulfase on growth in patients enrolled in HOS - the Hunter Outcome Survey which is a multinational observational database. As of Jan 2012, height data before treatment were available for 567 of 740 males followed prospectively after HOS entry. Cross-sectional analysis showed that short stature became apparent after approximately 8 years of age; before this, height remained within the normal range. Age-corrected standardized height scores (z-scores) before and after treatment were assessed using piecewise regression model analysis in 133 patients (8-15 years of age at treatment start; data available on ≥ 1 occasion within +/-24 months of treatment start; growth hormone-treated patients excluded). Results showed that the slope after treatment (slope=-0.005) was significantly improved compared with before treatment (slope=-0.043) (difference=0.038, p=0.004). Analysis of covariates (age at treatment start, cognitive involvement, presence of puberty at the start of ERT, mutation type, functional classification), showed a significant influence on growth of mutation type (height deficit in terms of z-scores most pronounced in patients with deletions/large rearrangements/nonsense mutations, p<0.0001) and age (most pronounced in the 12-15-year group, p<0.0001). Cognitive involvement, pubertal status at the start of ERT and functional classification were not related to the growth deficit or response to treatment. In conclusion, the data showed an improvement in growth rate in patients with Hunter syndrome following idursulfase treatment.

Three-dimensional study of nasopalatine canal morphology: a descriptive retrospective analysis using cone-beam computed tomography

PURPOSE For dental implant treatment planning and placement, a precise anatomic description of the nasopalatine canal (NC) is necessary. This descriptive retrospective study evaluated dimensions of the NC and buccal bone plate (BBP) and the tridimensional association of the anatomic variants of NC, using cone-beam computed tomography (CBCT). METHODS This study included 230 CBCTs. Sagittal slices were used for measurements of the NC and BBP and to evaluate shape and direction-course of the NC. Coronal slices were used to assess NC shape and axial slices to assess number of incisive foramina and foramina of Stenson. RESULTS Mean NC length was 12.34 ± 2.79 mm, statistically significant differences were detected between genders (p < 0.001). Mean BBP length was 20.87 ± 3.68 mm, statistically significant differences were found for the dental status (p < 0.001) and mean BBP width was 6.83 ± 1.28 mm, significant differences were detected between genders (p < 0.001). Mean nasopalatine angle was 73.33° ± 8.11°, significant differences were found in sagittal and coronal classifications. The most prevalent canal was: cylindrical sagittal shape (48.2 %); slanted-straight direction-course (57.6 %); Ya-type coronal shape (42.4 %); and one foramen incisive with two Stenson's foramina (1-2) (50.9 %). Sagittal shape was associated with sagittal direction-course (p < 0.001). Coronal shape was associated with axial classification (p < 0.001). CONCLUSIONS The NC anatomy is highly variable. Gender is related to the NC length and BBP width, while dental status is related to BBP length. There was an association between the different sagittal classifications of the NC and between the coronal shape and axial classification.

Tumour border configuration in colorectal cancer: proposal for an alternative scoring system based on the percentage of infiltrating margin.

AIMS Information on tumour border configuration (TBC) in colorectal cancer (CRC) is currently not included in most pathology reports, owing to lack of reproducibility and/or established evaluation systems. The aim of this study was to investigate whether an alternative scoring system based on the percentage of the infiltrating component may represent a reliable method for assessing TBC. METHODS AND RESULTS Two hundred and fifteen CRCs with complete clinicopathological data were evaluated by two independent observers, both 'traditionally' by assigning the tumours into pushing/infiltrating/mixed categories, and alternatively by scoring the percentage of infiltrating margin. With the pushing/infiltrating/mixed pattern method, interobserver agreement (IOA) was moderate (κ = 0.58), whereas with the percentage of infiltrating margins method, IOA was excellent (intraclass correlation coefficient of 0.86). A higher percentage of infiltrating margin correlated with adverse features such as higher grade (P = 0.0025), higher pT (P = 0.0007), pN (P = 0.0001) and pM classification (P = 0.0063), high-grade tumour budding (P < 0.0001), lymphatic invasion (P < 0.0001), vascular invasion (P = 0.0032), and shorter survival (P = 0.0008), and was significantly associated with an increased probability of lymph node metastasis (P < 0.001). CONCLUSIONS Information on TBC gives additional prognostic value to pathology reports on CRC. The novel proposed scoring system, by using the percentage of infiltrating margin, outperforms the 'traditional' way of reporting TBC. Additionally, it is reproducible and simple to apply, and can therefore be easily integrated into daily diagnostic practice.