Clinical exome sequencing ­ Norwegian findings.

BACKGROUND: New DNA-sequencing technology is revolutionising medical diagnostics. Through the use of exome sequencing, it is now possible to sequence all human genes in parallel. This technology has been widely used in research over the last few years and is now also being applied to diagnostics. The aim of this study was to systematically examine initial experiences with diagnostic exome sequencing in Norway. MATERIAL AND METHOD: This is a retrospective observational study of the results of all exome sequencing performed by the Section of Medical Genetics at Telemark Hospital between December 2012 and October 2014, and includes 125 persons in 46 families. The majority of these families were being investigated for a syndrome (n = 35, 76%) or neurological disease (n = 9, 20%). RESULTS: Exome sequencing detected pathogenic sequence variants in 15 of 46 probands, and variants of unknown significance in 12 probands. Of the 100 patients who stated their wishes regarding feedback of any incidental findings, six indicated that they did not wish to receive such information. There were no incidental findings in this study, but neither were such sequence variants actively looked for. INTERPRETATION: Exome sequencing can enable more patients with syndromes or neurological diseases to receive a causal diagnosis, and to receive this diagnosis at an earlier stage. However, the patients in this study were quite highly selected, and the results must therefore be interpreted with caution.

Hereditary peripheral neuropathies diagnosed by next-generation sequencing.

BACKGROUND: Next-generation sequencing (NGS) is a genetic technique used to determine the order of nucleotides in DNA. The technique has proved to be more efficient than the traditional method, Sanger sequencing, for sequencing multiple genes. NGS is now being used to diagnose disorders in which multiple genes are involved. This study has examined whether next-generation sequencing produces a greater number of positive diagnoses than its traditional counterpart in patients with suspected hereditary peripheral neuropathy. MATERIAL AND METHOD: This study is a retrospective review of samples from 103 patients investigated for hereditary peripheral neuropathy, received by Telemark Hospital in the period 2012-14. After exclusion of duplication/deletion of PMP22, 96 samples were analysed by NGS with physical enrichment of 52 hereditary peripheral neuropathy genes. RESULTS: A genetic cause was identified in 35 patients (34%) with peripheral neuropathy, of which 28 (27%) were point mutations identified by NGS. INTERPRETATION: Of the pathogenic point mutations identified in this study, 12 were in genes that would previously have been analysed by Sanger sequencing in our department, whereas 16 were in genes that would not previously have been tested.

Multilocus sequence typing and ftsI sequencing: a powerful tool for surveillance of penicillin-binding protein 3-mediated beta-lactam resistance in nontypeable Haemophilus influenzae.

BACKGROUND: Beta-lactam resistance in Haemophilus influenzae due to ftsI mutations causing altered penicillin-binding protein 3 (PBP3) is increasing worldwide. Low-level resistant isolates with the N526K substitution (group II low-rPBP3) predominate in most geographical regions, while high-level resistant isolates with the additional S385T substitution (group III high-rPBP3) are common in Japan and South Korea.Knowledge about the molecular epidemiology of rPBP3 strains is limited. We combined multilocus sequence typing (MLST) and ftsI/PBP3 typing to study the emergence and spread of rPBP3 in nontypeable H. influenzae (NTHi) in Norway. RESULTS: The prevalence of rPBP3 in a population of 795 eye, ear and respiratory isolates (99% NTHi) from 2007 was 15%. The prevalence of clinical PBP3-mediated resistance to ampicillin was 9%, compared to 2.5% three years earlier. Group II low-rPBP3 predominated (96%), with significant proportions of isolates non-susceptible to cefotaxime (6%) and meropenem (20%). Group III high-rPBP3 was identified for the first time in Northern Europe.Four MLST sequence types (ST) with characteristic, highly diverging ftsI alleles accounted for 61% of the rPBP3 isolates. The most prevalent substitution pattern (PBP3 type A) was present in 41% of rPBP3 isolates, mainly carried by ST367 and ST14. Several unrelated STs possessed identical copies of the ftsI allele encoding PBP3 type A.Infection sites, age groups, hospitalization rates and rPBP3 frequencies differed between STs and phylogenetic groups. CONCLUSIONS: This study is the first to link ftsI alleles to STs in H. influenzae. The results indicate that horizontal gene transfer contributes to the emergence of rPBP3 by phylogeny restricted transformation.Clonally related virulent rPBP3 strains are widely disseminated and high-level resistant isolates emerge in new geographical regions, threatening current empiric antibiotic treatment. The need of continuous monitoring of beta-lactam susceptibility and a global system for molecular surveillance of rPBP3 strains is underlined. Combining MLST and ftsI/PBP3 typing is a powerful tool for this purpose.

Sulfonamides as selective oestrogen receptor ß agonists.

A series of p-hydroxybenzenesulphonamides ERß receptor agonists were discovered and several compounds identified had excellent selectivity over the related ERα receptor. One of these, compound 11, had an interesting binding conformation determined by X-ray and represents an excellent starting point in the quest for further selective ERß agonists.

HINT1 neuropathy in Norway: clinical, genetic and functional profiling.

BACKGROUND: Autosomal recessive axonal neuropathy with neuromyotonia has been linked to loss of functional HINT1. The disease is particularly prevalent in Central and South-East Europe, Turkey and Russia due to the high carrier frequency of the c.110G > C (p.Arg37Pro) founder variant. RESULTS: In a cohort of 748 Norwegian patients with suspected peripheral neuropathy, we identified two seemingly unrelated individuals, compound heterozygous for a new variant (c.284G > A, p.Arg95Gln) and the most common pathogenic founder variant (c.110G > C, p.Arg37Pro) in the HINT1 gene. Probands presented with motor greater than sensory neuropathy of various onset, accompanied by muscle stiffness and cramps in the limbs. Furthermore, they displayed non-classical symptoms, including pain in the extremities and signs of central nervous system involvement. Haplotype analysis in both patients revealed a common chromosomal background for p.Arg95Gln; moreover, the variant was identified in Swedish carriers. Functional characterization in HINT1-knockout and patient-derived cellular models, and in HNT1-knockout yeast, suggested that the new variant is deleterious for the function of HINT1 and provided mechanistic insights allowing patient stratification for future treatment strategies. CONCLUSION: Our findings broaden the genetic epidemiology of HINT1-neuropathy and have implications for molecular diagnostics of inherited peripheral neuropathies in Scandinavia.

The Terrible Summer of 1952 When Polio Struck Our Family.

This is the story of my twin brother's struggle with polio. The story reflects the thoughts and feelings of Lyle and members of his family and describes how we all coped with the event.

The impact of pharmaceutical care practice on the practitioner and the patient in the ambulatory practice setting: twenty-five years of experience.

This manuscript reviews 25 years of experience that include developing the practice of pharmaceutical care and initiating new practices. The impact this practice has on practitioners in the ambulatory setting is described as well as data that reflect its clinical and economic impact. There is a great need to prepare new practitioners to provide pharmaceutical care. A focused training program was developed and delivered to over 300 practitioners. The practitioners were prepared by providing direct patient care. They learned the philosophy of pharmaceutical care practice, to identify, resolve and prevent drug therapy problems, to document care using a specially designed software program called the Assurance Pharmaceutical Care program. The practitioners who participated in the training program reported that the average amount of time spent with patients increased three-fold, they now see four times more patients than prior to training, and the number of new patients referred by physicians increased nine-fold as a result of the program. These practitioners have now provided care to more than 25,000 patients in their practices. These data have now been consolidated and analyzed, and a portion of these results is reported here. The clinical and economic outcomes from 2,985 adult patients, who received pharmaceutical care between January, 2000 and December, 2003, are presented. At the first assessment by the pharmaceutical care practitioner, 61% of the patients had one or more drug therapy problems identified and resolved. This resulted in an improvement in the clinical status or maintaining a stable status in 83% of the patients. The health care savings realized from pharmaceutical care were $1,134,162. This represented a benefit to cost ratio of 2:1. Physicians who collaborate with pharmaceutical care practitioners have validated the work of the practitioners, and patients are recognizing the benefits of pharmaceutical care.

High levels of multiresistance in quinolone resistant urinary tract isolates of Escherichia coli from Norway; a non clonal phenomen?

BACKGROUND: The problem of emerging ciprofloxacin resistance is compounded by its frequent association with multiresistance, the reason for which is not fully understood. In this study we compare multiresistance, clonal similarities and phylogenetic group in urinary tract isolates of Escherichia coli sensitive and resistant to the quinolone antimicrobials nalidixic acid and ciprofloxacin. RESULTS: Quinolone resistant isolates were more resistant to non-quinolone antibiotics than sensitive isolates, with resistance to ampicillin, mecillinam, sulphonamide, trimethoprim, tetracycline, kanamycin and chloramphenicol significantly increased. Fifty-one percent of quinolone-resistant isolates were multiresistant. Although multiresistance was most prevalent (63%) in isolates showing high-level ciprofloxacin resistance, it was still highly prevalent (41%) in nalidixic acid resistant isolates with low-level ciprofloxacin resistance. Multiresistance was more frequent among singleton isolates (61%) than clonal isolates (40%) of quinolone resistant Escherichia coli. Ciprofloxacin resistance was associated with certain specific clones, among them the globally distributed clonal Group A. However, there was no significant difference in the overall degree of clonality between quinolone sensitive and resistant isolates. Ciprofloxacin resistance was positively associated with phylogroup D and negatively associated with phylogroup B2. This correlation was not associated with clonal isolates. CONCLUSION: This study supports earlier findings of association between ciprofloxacin resistance and resistance to other antibiotics. The prevalence of multiresistance in quinolone-resistant isolates that have not yet developed high-level ciprofloxacin resistance suggest that multiresistance arises early in the development of quinolone resistance. This is consistent with exposure to quinolones causing quinolone resistance by mutations and mobilization of multiresistance elements by induction of the SOS response. The spread of clones seems to be less important than previously reported in regard to emergence of quinolone resistance and multiresistance as both are associated primarily with singleton isolates.

Genetic diagnosis of Charcot-Marie-Tooth disease in a population by next-generation sequencing.

Charcot-Marie-Tooth (CMT) disease is the most prevalent inherited neuropathy. Today more than 40 CMT genes have been identified. Diagnosing heterogeneous diseases by conventional Sanger sequencing is time consuming and expensive. Thus, more efficient and less costly methods are needed in clinical diagnostics. We included a population based sample of 81 CMT families. Gene mutations had previously been identified in 22 families; the remaining 59 families were analysed by next-generation sequencing. Thirty-two CMT genes and 19 genes causing other inherited neuropathies were included in a custom panel. Variants were classified into five pathogenicity classes by genotype-phenotype correlations and bioinformatics tools. Gene mutations, classified certainly or likely pathogenic, were identified in 37 (46%) of the 81 families. Point mutations in known CMT genes were identified in 21 families (26%), whereas four families (5%) had point mutations in other neuropathy genes, ARHGEF10, POLG, SETX, and SOD1. Eleven families (14%) carried the PMP22 duplication and one family carried a MPZ duplication (1%). Most mutations were identified not only in known CMT genes but also in other neuropathy genes, emphasising that genetic analysis should not be restricted to CMT genes only. Next-generation sequencing is a cost-effective tool in diagnosis of CMT improving diagnostic precision and time efficiency.

Simultaneous detection, typing and quantitation of oncogenic human papillomavirus by multiplex consensus real-time PCR.

A consensus multiplex real-time PCR test (PT13-RT) for the oncogenic human papillomavirus (HPV) types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 66 is described. The test targets the L1 gene. Analytical sensitivity is between 4 and 400 GU (genomic units) in the presence of 500 ng of human DNA, corresponding to 75,000 human cells. HPV types are grouped into multiplex groups of 3 or 4 resulting in the use of 4 wells per sample and permitting up to 24 samples per run (including controls) in a standard 96-well real-time PCR instrument. False negative results are avoided by (a) measuring sample DNA concentration to control that sufficient cellular material is present and (b) including HPV type 6 as a homologous internal control in order to detect PCR inhibition or competition from other (non-oncogenic) HPV types. Analysis time from refrigerator to report is 8 h, including 2.5 h hands-on time. Relative to the HC2 test, the sensitivity and specificity were respectively 98% and 83%, the lower specificity being attributable to the higher analytical sensitivity of PT13-RT. To assess type determination comparison was made with a reversed line-blot test. Type concordance was high (κ=0.79) with discrepancies occurring mostly in multiple-positive samples.

Emergence of fluoroquinolone-resistant clonal group A: clonal analysis of Norwegian and Russian E. coli isolates.

We describe a study of urinary tract and intestinal isolates of Escherichia coli from Norway and Russia using automated ribotyping, single nucleotide polymorphism analysis for clonal group A (CgA) supplemented with phylogrouping, virulence gene profiling and resistance profiling. CgA comprised 19% of the Norwegian UTI isolates from 2001. Two highly multiresistant fluoroquinolone-resistant CgA isolates were found. Ribotypes clustered into four major and six minor groups (ribogroups). Fluoroquinolone-resistant isolates and phylogroups A and B1 were associated with ribogroup (R)A. Ribogroup (R)B predominated among Russian UTI isolates and was predominantly phylogroup A and depleted in P-fimbriae. Ribogroup (R)C predominated among Norwegian UTI isolates and was rich in virulence factors (S-fimbriae, haemagglutinin and haemolysin) and predominantly phylogroup B2 and D. Ribogroup (R)G was associated with CgA and predominantly phylogroup D. Ribogroups (R)D, (R)E and (R)F had too few members for statistical analysis. The correlation between ribotype and phylogenetic group was not as strong as reported in other studies.

Drug therapy problems found in ambulatory patient populations in Minnesota and South Australia.

OBJECTIVE: To compare drug therapy problems identified by pharmacists in two patient samples, the Minnesota Sample and the South Australian Sample. METHODS: Two patient samples were selected for this comparison. Both sets of patients received pharmaceutical care services from pharmaceutical care practitioners between March 1999 and February 2000. The two databases were then compared for common drug therapy problems. MAIN OUTCOME MEASURE: Comparison of drug therapy problems in the two samples. RESULTS: Both patient samples included patients who were 40 years of age or older. The Minnesota Sample included 1,598 individual patients, of whom 70% experienced one or more drug therapy problems at some time during their care. The South Australian Sample included a total of 982 patients of whom 90% experienced one or more drug therapy problems at some time during their care. Conditions common to both patient samples include hypertension, diabetes, arthritis, ischemic heart disease, and osteoporosis. Frequently occurring drug therapy problems in the Minnesota Sample included the need for additional drug therapy, dosage too low and non-compliance and in the South Australian Sample included non-compliance, additional drug therapy and ineffective drug therapy. Frequent drug therapy problems associated with medical conditions in the Minnesota Sample included addition of new therapies for conditions such as arthritis, hypertension, hyperlipidemia and allergic rhinitis, while for the South Australian Sample included compliance issues with conditions such as asthma, diabetes mellitus, angina and digestive disorders. Frequent drug therapy problems with associated drug classes in the Minnesota Sample included additional therapy for classes such as salicylates and calcium supplements, while in the South Australian Sample included the need for therapy for pneumococcal vaccines, salicylates, calcium supplements and tetanus vaccines. CONCLUSION: These data demonstrate that this age group has significant drug therapy problems and therefore emphasize the need for pharmaceutical care services in this population. The provision of pharmaceutical care by experienced practitioners can result in improved recognition of the full range of drug therapy problems confronting patients. Analyses such as those presented here provide information to better focus the training of practitioners based on the most frequently encountered health problems and the nature of common drug therapy problems in the community setting.

Consistent standards in medication use: the need to care for patients from research to practice.

OBJECTIVE: To propose adoption of practice standards for pharmacists based on the principles of pharmaceutical care that are parallel to internationally accepted ethical precepts governing clinical research. DATA SOURCES: Relevant literature selected by the authors. SUMMARY: Pharmaceutical care practice standards can create a continuum of high quality care for patients from research through practice and are presented as a rational solution to managing the benefits and risks of medication use. By implementing these practice standards, patients are empowered to become active participants in the treatment process, knowledge of drug effectiveness and safety is increased, and the pharmaceutical care practitioner's responsibilities are delineated. More than a quarter century ago, the research community adopted the ethical principles of respect for persons, beneficence, and justice, as outlined in the Belmont Report: Ethical Principles and Guidelines for the Protection of Human Subjects of Research. Under these guidelines, research subjects are considered participants, knowledge of medication efficacy and safety has increased, and investigator responsibilities have been defined. However, these guidelines only apply to the life cycle of a drug before approval by the Food and Drug Administration. Once the product is released for general use, fewer standards are applied. Pharmacy has the opportunity to establish parallel standards for the clinical use of medications in patients by establishing patient care practices in consonance with pharmaceutical care practice. CONCLUSION: Pharmaceutical care practitioners need to apply new practice standards that allow them to contribute meaningfully to appropriate, effective, safe, and convenient drug therapy for all patients. Such pharmaceutical care practice standards could ensure consistent vigilance throughout the life cycle of the drug product and result in rational, appropriate, effective, safe, and convenient drug therapy for all patients.

Critically examining pharmaceutical care.

In the past decade, growing numbers of practitioners worldwide have adopted pharmaceutical care as an integral component of pharmacy practice. Established models of pharmaceutical care can reduce the burden of preventable drug therapy problems, but this promise has not yet been realized. Although many challenges remain, the profession has key resources to expand and improve the delivery of pharmaceutical care.