Two-stage tuberculosis diagnostics: combining centrifugal microfluidics to detect TB infection and Inh and Rif resistance at the point of care with subsequent antibiotic resistance profiling by targeted NGS

Globally, tuberculosis (TB) remains the deadliest bacterial infectious disease, and spreading antibiotic resistances is the biggest challenge for combatting the disease. Rapid and comprehensive diagnostics including drug susceptibility testing (DST) would assure early treatment, reduction of morbidity and the interruption of transmission chains. To date, rapid genetic resistance testing addresses only one to four drug groups while complete DST is done phenotypically and takes several weeks. To overcome these limitations, we developed a two-stage workflow for rapid TB diagnostics including DST from a single sputum sample that can be completed within three days. The first stage is qPCR detection of M. tuberculosis complex (MTBC) including antibiotic resistance testing against the first-line antibiotics, isoniazid (Inh) and rifampicin (Rif). The test is automated by centrifugal microfluidics and designed for point of care (PoC). Furthermore, enriched MTBC DNA is provided in a detachable sample tube to enable the second stage: if the PCR detects MTBC and resistance to either Inh or Rif, the MTBC DNA is shipped to specialized facilities and analyzed by targeted next generation sequencing (tNGS) to assess the complete resistance profile. Proof-of-concept testing of the PoC test revealed an analytical sensitivity of 44.2 CFU ml-1, a diagnostic sensitivity of 96%, and a diagnostic specificity of 100% for MTBC detection. Coupled tNGS successfully provided resistance profiles, demonstrated for samples from 17 patients. To the best of our knowledge, the presented combination of PoC qPCR with tNGS allows for the fastest comprehensive TB diagnostics comprising decentralized pathogen detection with subsequent resistance profiling in a facility specialized in tNGS.

Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country

Whole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implementation in such a setting. WGS was implemented in the Kyrgyz Republic. We estimated needs of up to 55 TB-WGS per week and chose the MiSeq platform (Illumina, USA) because of its capacity of up to 60 TB-WGS per week. The project's timeline was completed in 93-weeks. Costs of large equipment and accompanying costs were 222,065 USD and 8462 USD, respectively. The first 174 WGS costed 277 USD per sequence, but this was skewed by training inefficiencies. Based on real prices and presuming optimal utilization of WGS capacities, WGS costs could drop to 167 and 141 USD per WGS using MiSeq Reagent Kits v2 (500-cycles) and v3 (600-cycles), respectively. Five trainings were required to prepare the staff for autonomous WGS which cost 48,250 USD. External assessment confirmed excellent performance of WGS by the Kyrgyz laboratory in an interlaboratory comparison of 30 M. tuberculosis genomes showing complete agreeance of results.

[Therapy-resistant pyoderma gangrenosum--treatment with mycophenolate mofetil and cyclosporine A]

A 68-year old woman presented with ulcerations on the calves that had occurred spontaneously. The very painful lesions both clinically and histologically showed the characteristics of pyoderma gangrenosum. During hospitalization she was treated with corticosteroids (oral, i.v., topically), clofazimine, cyclophosphamide, intravenous immune globulin, cyclosporine (oral, local), dapsone, thalidomide and sodium cromoglycate (topically) without any benefit. Finally, when treated with mycophenolate mofetil (CellCept) (oral) and cyclosporine (oral), her skin lesions showed continuous improvement. The topical application of thrombocytic growth factors (cytokines) probably accelerated the granulation. Eight weeks after initiating this treatment the lesions could be covered with split thickness skin grafts. Our observation suggests that mycophenolate mofetil, a novel immunosuppressive agent which has thus far been used almost exclusively in transplantation medicine, may be an effective therapeutic modality in combination with cyclosporine A for the treatment of pyoderma gangrenosum.

Microdissection-based analysis of mature ovarian teratoma

The genotypic features of mature ovarian teratomas (MOTs) are controversial. Early studies detected a homozygous genotype in MOTs suggesting that these tumors are composed of germ cells that have undergone meiosis I. Other studies, however, revealed a heterozygous genotype in a substantial proportion of MOTs suggesting an origin either from premeiotic germ cells or from a somatic cell line. In view of the complex morphology of MOTs and to increase the sensitivity of teratoma genotyping, we applied tissue microdissection before genetic analysis of teratomatous tissue. This approach allowed selective analysis of different heterotopic tissue elements as well as the lymphoid tissues within MOTs the origin of which is unknown. After DNA extraction, the tissue samples were polymerase chain reaction amplified using a random panel of highly informative genetic markers for different chromosomes to evaluate heterozygosity versus homozygosity. In all seven cases that were analyzed, heterotopic tissues consistently revealed a homozygous genotype with several markers; in two cases, heterozygosity was detected with a single marker, indicating a meiotic recombination event. Lymphoid aggregates within MOTs were heterozygous and derived from host tissue rather than from teratomatous growth. However, well differentiated thymic tissue was consistently homozygous, suggesting lymphoid differentiation capability of MOTs. We conclude that potential pitfalls in genotyping of teratomas including meiotic recombination and host cell participation can be avoided by a microdissection-based approach in combination with a panel of genetic markers.

Potent vasodilatory with minor cardiodepressant actions of mibefradil in human cardiac tissue

1. The present study compared the cardiovascular effects of mibefradil (MIB), a novel Ca2+-channel antagonist with high selectivity for T-type Ca2+-channels to the effect of the L-type Ca2+-channel-antagonists nifedipine (NIF) and diltiazem (DIL) in left ventricular myocardium and coronary arteries of hearts obtained from patients suffering from dilated cardiomyopathy (NYHA IV). Right atrial myocardium from patients undergoing aortocoronary bypass surgery without signs of cardiac failure was studied as well. 2. NIF and DIL (100 micromol l(-1)) completely depressed force of contraction (FOC) in electrically driven left ventricular myocardium (NIF 6.5+/-1.4% and DIL 7.1+/-1.2% of control), whereas a similar concentration of MIB only reduced force of contraction to 55.1+/-4.0% of the basal FOC. The negative inotropic potency as measured by the concentration needed to reduce basal FOC for 25% was NIF (0.0095 micromol l(-1))>DIL (0.041 micromol l(-1))>MIB (9.47 micromol l(-1)). 3. All three Ca2+-channel antagonists were more potent in human atrial compared to human left ventricular myocardium to reduce FOC. 4. The rank order of Ca+-antagonistic moiety as measured by the decrease of the intracellular Ca2+-transient (fura-2 ratio method) was NIF>DIL>MIB. 5. All Ca2+-channel antagonists completely relaxed human coronary arteries (% of papaverine effect: MIB 81.7+/-5.5%, DIL 91.3+/-0.9%, NIF 96.4+/-3.7%) precontracted with PGF2alpha (0.3 micromol l(-1)). The rank order of vasodilatory potency was NIF (EC50; 0.02 micromol l(-1))>DIL (0.13 micromol l(-1))>MIB (2.05 micromol l(-1)). 6. The vasoselectivity measured by the ratio of the concentration needed to achieve a 25% decrease in force and the concentration needed for 25% vasodilatation was 316 for MIB, 1.5 for NIF and 1.0 for DIL. 7. The present study provides evidence that blockade of T-type Ca2+-channels (e.g. mibefradil) results in potent vasodilatory properties with only minor cardiodepressant effects.

[Masked course of Whipple disease with uveitis, infection, endocardial involvement and abdominal lymphomas--case report and review of the literature]

Whipple's disease is a systemic disease which may virtually affect any organ system, but in many cases it involves the small intestine causing gastrointestinal symptoms. The differential diagnosis is difficult since symptoms may be nonspecific. We report the case of a 44-year old white male patient with a history of migrating arthralgia and chronic fatigue. The patient newly developed an uveitis and underwent a vitrectomy; the further clinical work-up including gastroscopy with intestinal biopsy revealed no sufficient diagnosis. Subsequently, the patient's condition deteriorated with marked weight loss, fever and progressive weakness. An anaerobic sepsis with a corynebacterium was confirmed and with i.v.-antibiotics the patients's condition improved markedly. The further examinations disclosed enlarged mesenteric lymph nodes and the involvement of other organs (endocard, liver). CT-guided biopsy only showed fatty degeneration, but operative adenectomy confirmed Whipple's disease. The patient remained without relapse on long-term antibiotic treatment with doxycycline until today. Obviously, in our case the intestinal biopsies failed to detect Whipple's disease after the successful initiation of antibiotic treatment. In the absence of gastrointestinal findings and with concomitant secondary diseases the definitive diagnosis can be difficult. In addition, the previous uveitis and the endocardial involvement are most interesting.

Symptom patterns of alcoholism in a northern Ontario population

Alcoholism is noted to be a common problem in Canada and particularly in native populations. We report here a survey of the frequency of evidence of alcoholism over a period of four months in a relatively isolated Northern Ontario population in which more than 80% were either status Indians or of partly Indian origin. Using questionnaire methods, "definite" alcoholism was found to affect 27% of adults seen at a clinic and probable alcoholism affected another 20%. This gives a minimum prevalence of 14.6% of the local adult population over a four month period on the basis merely of examination of less than one third of the adults in the community. Blackouts, tremors, bad temper, chest pain, unsteadiness, loss of appetite, vomiting, sadness and stomach pain occurred significantly more often in the alcoholic patients. Stomach pain, loss of appetite and vomiting were less prominent with alcoholism in this population than in a Southern population. The findings indicate the importance in general practice of looking for alcoholism, the ease with which this may be undertaken with a few very simple short questions and the importance of some characteristic patterns, especially blackouts, shakiness and unsteadiness as one pattern and stomach pain and other gastro-intestinal symptoms as another pattern.

Biochemistry of the autolytic processes in Antarctic krill post mortem. Autoproteolysis

1. Autoproteolysis post mortem was examined at 0 degree C by following the changes in the major classes of krill (Euphausia superba and Euphausia crystallorophias) proteins and by liberation of peptides and free amino acids, and was based on experiments conducted on board expedition vessels in the Antarctic. 2. Primarily salt-soluble proteins were broken down during the first week of incubation, whereas water-soluble and insoluble proteins were degraded to a much smaller extent. The enzymes responsible for the hydrolysis presumably originate primarily from the digestive apparatus of the krill. 3. In general, the individual amino acids were released at rates corresponding to their relative occurrence in the bulk protein of the krill. Alanine was liberated in larger amounts than would be expected from the composition of the krill protein, and was evidently formed also by reactions other than proteolysis. Glutamic acid, and certain amino acids which presumably occur with high frequency adjacent to glumatic acid residues in the krill protein, were liberated only to a limited extent, and accumulated in smaller peptides. 4. During proteolysis, arginine seemed to be converted to some degree into ornithine, and on prolonged incubation conversion of arginine and lysine into their corresponding decarboxylation products, agmatine and cadaverine, appeared to take place.

Proteases of Antarctic krill--a new system for effective enzymatic debridement of necrotic ulcerations

The Antarctic krill (Euphausia superba) possesses an "over-dimensioned' digestive system, which is of vital importance for the survival of this euphaucean shrimp in the extreme marine environment. The isolated enzymes contain a well-balanced mixture of both endo- and exopeptidases, assuring fast and complete breakdown of proteinaceous material. These unique properties have now been shown to be extremely valuable for the effective removal of necrotic debris, fibrin or blood crusts in vitro. Therefore the krill enzymes should be considered as an important resource in the future management of necrotic wounds.

Lipids of North Atlantic krill

The seasonal variations in the total lipid content, lipid class composition, fatty acid composition, and fatty alcohol composition of Meganyctiphanes norvegica (M. Sars), Thysanoessa inermis (Krøyer), and T. raschii (M. Sars) have been examined. The total lipid content was highest in the autumn and early winter months and lowest in the spring. In M. norvegica, triacylglycerols served as the only depot lipids, whereas in T. inermis and T. raschii triacylglycerols, wax esters, and glycerophospholipids varied in proportion to the total lipid content. This suggests that glycerophospholipids, as well as wax esters and triacylglycerols, constitute depot lipids in these species. Wax esters and glycerophospholipids were the dominating depot lipids in T. inermis, whereas triacylglycerols and glycerophospholipids were most important in T. raschii. Results suggest that non-depot glycerophospholipids may constitute 3.5-4.5% of the dry weight of the three species of krill examined. T. inermis and T. raschii, from the same catches, had very similar fatty acid compositions for each of the major lipid classes, with the exception of a few minor fatty acids. The major lipid classes in all three species showed complex seasonal variations in the content of the fatty acids that typically reflect the diet, particularly in the case of the triacylglycerols. The results suggest that all the species examined are more herbivorous during the summer than during the autumn and winter. M. norvegica seemed to be significantly more carnivorous than the two Thysanoessa species. The degree of incorporation of individual fatty acids from the diet is probably specific for each lipid class in each krill species. The proportion of polyenoic fatty acids in the glycerophospholipids and the proportion of monoenoic fatty acids in the wax esters may be of importance for the temperature adaptation of T. inermis and T. raschii.