More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data.
Organisms of the candidate phylum termite group 1 (TG1) are regularly encountered in termite hindguts but are present also in many other habitats. Here, we report the complete genome sequence (1.64 Mbp) of “Elusimicrobium minutum” strain Pei191T, the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut, and we discuss the findings in light of physiological data. E. minutum has all genes required for uptake and fermentation of sugars via the Embden-Meyerhof pathway, including several hydrogenases, and an unusual peptide degradation pathway comprising transamination reactions and leading to the formation of alanine, which is excreted in substantial amounts. The presence of genes encoding lipopolysaccharide biosynthesis and the presence of a pathway for peptidoglycan formation are consistent with ultrastructural evidence of a gram-negative cell envelope. Even though electron micrographs showed no cell appendages, the genome encodes many genes putatively involved in pilus assembly. We assigned some to a type II secretion system, but the function of 60 pilE-like genes remains unknown. Numerous genes with hypothetical functions, e.g., polyketide synthesis, nonribosomal peptide synthesis, antibiotic transport, and oxygen stress protection, indicate the presence of hitherto undiscovered physiological traits. Comparative analysis of 22 concatenated single-copy marker genes corroborated the status of “Elusimicrobia” (formerly TG1) as a separate phylum in the bacterial domain, which was so far based only on 16S rRNA sequence analysis.
Management of airway infections caused by Pseudomonas aeruginosa is a serious clinical challenge, but little is known about the microbial ecology of airway infections in intubated patients. We analyzed bacterial diversity in endotracheal aspirates obtained from intubated patients colonized by P. aeruginosa by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment. Bacterial 16S rRNA genes were absent from aspirates obtained from patients briefly intubated for elective surgery but were detected by PCR in samples from all patients intubated for longer periods. Sequencing of 16S rRNA clone libraries demonstrated the presence of many orally, nasally, and gastrointestinally associated bacteria, including known pathogens, in the lungs of patients colonized with P. aeruginosa. PhyloChip analysis detected the same organisms and many additional bacterial groups present at low abundance that were not detected in clone libraries. For each patient, both culture-independent methods showed that bacterial diversity decreased following the administration of antibiotics, and communities became dominated by a pulmonary pathogen. P. aeruginosa became the dominant species in six of seven patients studied, despite treatment of five of these six with antibiotics to which it was sensitive in vitro. Our data demonstrate that the loss of bacterial diversity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with P. aeruginosa. Interestingly, PhyloChip analysis demonstrated reciprocal changes in abundance between P. aeruginosa and the class Bacilli, suggesting that these groups may compete for a similar ecological niche and suggesting possible mechanisms through which the loss of microbial diversity may directly contribute to pathogen selection and persistence.
A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample. The computational resources and bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis. It was hypothesized that an online tool could be developed to efficiently align thousands of 16S rRNA genes via the NAST (Nearest Alignment Space Termination) algorithm for creating multiple sequence alignments (MSA). The tool was implemented with a web-interface at . Each user-submitted sequence is compared with Greengenes' ‘Core Set’, comprising ∼10 000 aligned non-chimeric sequences representative of the currently recognized diversity among bacteria and archaea. User sequences are oriented and paired with their closest match in the Core Set to serve as a template for inserting gap characters. Non-16S data (sequence from vector or surrounding genomic regions) are conveniently removed in the returned alignment. From the resulting MSA, distance matrices can be calculated for diversity estimates and organisms can be classified by taxonomy. The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles.
Bacteria phenotypically resembling members of the phylogenetically distinct planctomycete group of the domain Bacteria were isolated from postlarvae of the giant tiger prawn, Penaeus monodon. A selective medium designed in the light of planctomycete antibiotic resistance characteristics was used for this isolation. Planctomycetes were isolated from both healthy and monodon baculovirus-infected prawn postlarvae. The predominant colony type recovered from postlarvae regardless of viral infection status was nonpigmented. Other, less commonly observed types were pink or orange pigmented. A planctomycete-specific 16S rRNA-directed probe was designed and used to screen the isolates for their identity as planctomycetes prior to molecular phylogenetic characterization. 16S rRNA genes from nine prawn isolates together with two planctomycete reference strains (Planctomyces brasiliensis and Gemmata obscuriglobus) were sequenced and compared with reference sequences from the planctomycetes and other members of the domain Bacteria. Phylogenetic analyses and sequence signatures of the 16S rRNA genes demonstrated that the prawn isolates were members of the planctomycete group. Five representatives of the predominant nonpigmented colony type were members of the Pirellula group within the planctomycetes, as were three pink-pigmented colony type representatives. Homology values and tree topology indicated that representatives of the nonpigmented and pink-pigmented colony types formed two discrete clusters within the Pirellula group, not identical to any known Pirellula species. A sole representative of the orange colony type was a member of the Planctomyces group, virtually identical in 16S rDNA sequence to P. brasiliensis, and exhibited distinctive morphology.
The bacterial community structures of phosphate- and non-phosphate-removing activated sludges were compared. Sludge samples were obtained from two sequencing batch reactors (SBRs), and 16S rDNA clone libraries of the bacterial sludge populations were established. Community structures were determined by phylogenetic analyses of 97 and 92 partial clone sequences from SBR1 (phosphate-removing sludge) and SBR2 (non-phosphate-removing sludge), respectively. For both sludges, the predominant bacterial group with which clones were affiliated was the beta subclass of the proteobacteria. Other major groups represented were the alpha proteobacterial subclass, planctomycete group, and Flexibacter-Cytophaga-Bacteroides group. In addition, several clone groups unaffiliated with known bacterial assemblages were identified in the clone libraries. Acinetobacter spp., thought to be important in phosphate removal in activated sludge, were poorly represented by clone sequences in both libraries. Differences in community structure were observed between the phosphate- and non-phosphate-removing sludges; in particular, the Rhodocyclus group within the beta subclass was represented to a greater extent in the phosphate-removing community. Such differences may account for the differing phosphate-removing capabilities of the two activated sludge communities.
Heterotrophic bacteria from structural surfaces, drain pan water, and the airstream of a well-maintained air-handling system with no reported building-related illness were enumerated. Visually the system appeared clean, but large populations of bacteria were found on the fin surface of the supply-side cooling coils (10(5) to 10(6) CFU cm-2), in drain pan water (10(5) to 10(7) CFU ml-1), and in the sump water of the evaporative condenser (10(5) CFU ml-1). Representative bacterial colony types recovered from heterotrophic plate count cultures on R2A medium were identified to the genus level. Budding bacteria belonging to the genus Blastobacter dominated the supply surface of the coil fins, the drain pan water, and the postcoil air. These data and independent scanning electron microscopy indicated that a resident population of predominantly Blastobacter bacteria was present as a biofilm on the supply-side cooling coil fins.
Animal studies have demonstrated that synchronised coronary sinus retroperfusion with arterial blood can provide effective perfusion of ischaemic myocardium. Preliminary clinical studies have shown that the technique can also be used with safety in human beings, and in the present study its effectiveness was assessed in three patients undergoing repeated coronary artery occlusions during percutaneous transluminal coronary angioplasty. Arterial blood was removed via an 8F catheter positioned in the femoral artery and delivered by a retroperfusion pumping system to a 7F retroperfusion balloon catheter positioned in the anterior cardiac vein. Ischaemia-related indices were monitored both before and during coronary sinus retroperfusion. These indices included high fidelity left ventricular pressure recordings and pressure derived indices (including velocities of isovolumic contraction and relaxation), as well as electrocardiographic changes and symptoms. Analysis of these variables showed that the ischaemic changes induced during coronary artery occlusion were not prevented by this type of coronary sinus retroperfusion. There was no major complication in any of the patients. It may be that adaptation of the technique or the use of alternative end points will establish a benefit, but further modifications of the delivery system are necessary for effective clinical use.
Reintervention was required in 123 (12%) individuals during a follow up (mean 7.5 years, range 5-14.5) of 1041 patients with consecutive, isolated, first aortocoronary bypass operations. In 89 patients the intervention was a repeat bypass operation, in 24 it was angioplasty, and 10 had both. Procedure related mortality was significantly higher at reintervention (5.6%) than at the primary operation (1.2%). Survival probability after a single bypass procedure was 90% at six years and 82(3)% at nine years. Corresponding figures six and nine years after reintervention were 89(6)% and 87(7)% respectively. Stepwise multivariate analysis showed that survival was significantly correlated with left ventricular function (rate ratio 1.82) and with extent of vascular disease (rate ratio 1.80) but not with reintervention (rate ratio 1.45). Symptomatic improvement occurred in 89% of the survivors with or without reintervention. Repeat procedures are often necessary after coronary artery bypass grafting but they appear to provide appreciable relief of symptoms without reducing any long term improvement in survival brought about by the original operation.
The prognostic value of QRS score (Selvester), ST depression, ST elevation, extrasystoles, P terminal force in V1, and QTc derived from the predischarge 12 lead electrocardiogram was assessed after myocardial infarction in 474 patients without intraventricular conduction defects, ventricular hypertrophy, or atrial fibrillation. The usefulness of these results in risk assessment was compared with that of other clinical data. During follow up 45 patients died. Logistic regression analysis showed that QRS score, ST depression, and QTc were independently predictive of cardiac mortality. When multivariate analysis was applied to clinical and electrocardiographic data together, however, the 12 lead electrocardiogram did not provide independent information additional to that provided by other routine clinical findings and laboratory tests such as a history of previous myocardial infarction, clinical signs of persistent heart failure, indication for digitalis or antiarrhythmic drugs at discharge, and enlarged heart on chest x ray. In conclusion, the electrocardiogram has important prognostic value; however, it is not powerful enough to further improve the risk assessment of post-infarction patients.
The effects of DEHP on sperm morphology and on peripheral blood micronuclei were studied for 12 weeks following five subacute IP injections of DEHP at 1/6, 1/12, and 1/60 of the LD50 per day. Sperm morphology was examined in both adult mice and rats, while peripheral blood micronuclei were scored in mice up to 4 weeks after treatment. In mice, DEHP at 1/6 LD50 significantly depressed body weight gain for up to 12 weeks after treatment, and reduced epididymal sperm number by 4 weeks. Numbers of morphologically abnormal sperm did not differ from controls in the 12 weeks following treatment. In addition, DEHP did not increase the numbers of peripheral blood micronuclei. Studies in the rat indicated that exposure to doses of 1/6 and 1/12 of the LD50 per day of DEHP resulted in a reduced gain in body weight compared to controls. Testis weight, sperm number, and numbers of morphologically abnormal sperm were unaffected by DEHP following treatment. In separate experiments, DEHP did not induce sister chromatid exchange (SCE) or DNA damage in Chinese hamster ovary (CHO) cells. Although DEHP is known to cause testicular atrophy in rats and to a lesser extent in mice, it did not cause an increase in abnormal sperm in either species. Together with the CHO and micronucleus data, these findings suggest that DEHP has a low probability of causing genetic damage capable of being transmitted through the male germ line.
Of 510 patients admitted to hospital with acute myocardial infarction, 34 had coronary artery bypass grafting before discharge (6-43 days (median 20) after infarction). The patients who were given grafts generally had a smaller infarction with less functional impairment than the 476 patients who were not. The outcome of coronary artery bypass grafting was investigated in a retrospective matched pair study. Patients were matched on the basis of the presence of postinfarction angina, left ventricular ejection fraction, location of the infarction, peak creatine kinase activity, Killip clinical class, and severity of coronary disease with 34 patients who were given medical treatment only. At one year follow up fewer of the operated patients had symptoms than did the matched non-operated patients. Survival at one year in the operated and non-operated groups respectively was 94% vs 91%; angina within one year occurred in 3% vs 68%; congestive heart failure in 3% vs 6%; and 0% vs 32% were referred for later bypass grafting or coronary angioplasty. It is concluded that coronary artery bypass grafting can be performed safely soon after myocardial infarction provided that left ventricular function is not seriously compromised. Such treatment is more effective than medical treatment for relief of angina during the first year after infarction.
The value of a QRS scoring system derived from 12 lead electrocardiograms to estimate left ventricular ejection fraction was assessed in a prospective study of 285 hospital survivors of myocardial infarction. In these patients both the QRS score and ejection fraction were measured by radionuclide ventriculography at discharge. The correlation between ejection fraction and QRS score was weak. In 22 patients who died during six to 12 months follow up the ability of the ejection fraction and QRS score to predict mortality was assessed in terms of sensitivity, specificity, predictive value of a positive and negative test, and efficiency. For ejection fraction less than 40% and a QRS score greater than or equal to 6 sensitivity was respectively 73% and 64%, specificity 73% and 56%, predictive value of a positive test 18% and 11%, predictive value of a negative test 97% and 95%, and efficiency 73% and 56%. Both ejection fraction and QRS score may be used to identify patients at low and high risk during one year follow up, but, contrary to initial expectations, the QRS score appears to be of little value in estimating ejection fraction and is less accurate than ejection fraction in predicting late survival in hospital survivors of myocardial infarction.
Restenosis of the dilated vessel after percutaneous transluminal coronary angioplasty can be detected by non-invasive procedures but their ability to predict later restenosis soon after a successful angioplasty as well as recurrence of angina has not been assessed. A maximal exercise test and myocardial thallium perfusion scintigraphy were, therefore, performed in 91 asymptomatic patients a median of 5 weeks after they had undergone a technically successful angioplasty. Primary success of the procedure was confirmed by the decrease in percentage diameter stenosis from 64(12)% to 30(13)% as measured from the coronary angiograms and in the trans-stenotic pressure gradient (normalised for mean aortic pressure) from 0.61(0.16) to 0.17(0.09). A clinical follow up examination (8.6(4.9) months later) was carried out in all patients and a late coronary angiogram obtained in 77. The thallium perfusion scintigram showing the presence or absence of a reversible defect was highly predictive for restenosis whereas the exercise test was not. The positive predictive value of an abnormal scintigram was 82% compared with 60% for the exercise test (ST segment depression/or angina or both at peak workload). Angina or a new myocardial infarction occurred in 60% of patients with abnormal and in 21% of patients with normal scintigrams.
The relative merits of resting ejection fraction measured by radionuclide angiography and predischarge exercise stress testing were compared for predicting prognosis in hospital survivors of myocardial infarction. Two hundred and fourteen survivors of myocardial infarction out of 338 consecutive patients with acute myocardial infarction were studied over a 14 month period. Hospital mortality was 13% (45 of 338) whereas 19 additional patients out of 214 died in the subsequent year (9%). High, intermediate, and low risk groups could be identified by left ventricular ejection fraction measurement. Mortality was 33% for nine patients with an ejection fraction less than 20%, 19% for 58 patients with an ejection fraction between 20% and 39%, and 3% for 147 patients with an ejection fraction greater than 40%. Mortality was high (23%) in 47 patients who were unable to perform the stress test because of heart failure (19) or other limitations (28). The patients could be stratified further into intermediate and low risk groups according to the increase in systolic blood pressure during exercise: six deaths occurred in 46 patients with a blood pressure increase of less than 30 mm Hg and two deaths occurred in 121 patients with an increase greater than or equal to 30 mm Hg. Maximum workload, angina, ST changes, and ventricular arrhythmias were less predictive than blood pressure changes. It is concluded that the prognostic value of radionuclide angiography at rest and of symptom limited exercise testing is similar. The latter investigation should be the method of choice since it provides more specific information for patient management.
In order to assess the value of haemodynamic monitoring in the coronary care unit for long term prognosis after recovery of an acute myocardial infarction, the records of two groups of consecutive patients were reviewed retrospectively. From 254 patients, 32 (13%) died in the hospital and nine patients had to be excluded from subsequent follow-up for various reasons. Four year mortality among the 213 patients who were discharged from the hospital and could be followed up was 26%. Of the haemodynamic variables measured on admission a high pulmonary capillary wedge pressure, exceeding 18 mmHg, and a low mixed venous oxygen saturation, less than 60%, were not only associated with a high hospital but also with a high four year mortality, whereas a low systolic blood pressure (less than 100 mmHg), an important prognosticator during admission to hospital, was only of minor significance thereafter. A negative value on admission of a specific index 0.24 X systolic blood pressure (mmHg) -0.217 X pulmonary capillary wedge pressure (mmHg)+0.234 X mixed venous oxygen saturation (%)-13.1 developed for the prediction of short term survival was also associated with a much higher four year mortality than a positive value. Low cardiac index on admission could be correlated with high mortality during the first two years after discharge, whereas only 9% of patients with a higher cardiac index died. Haemodynamic monitoring in the coronary care unit is thus not only relevant for the immediate prognosis, but a high mortality risk during hospital stay persists for several years after discharge.
Of 1041 patients with consecutive aortocoronary bypass operations, 53 (5.1%) underwent reoperation during a mean follow-up time of three and a half years. The operative mortality of first operations was 1.2%, and of reoperations 3.8%. The anatomical reason for reoperation was failure of the bypass graft in 41 (77%) patients, which in 18 was accompanied by progression of disease. Progression alone was seen in seven (13%). When symptoms occurred within six months after the first operation, failure of the bypass graft(s) was nearly always found--in 32 out of 36 instances. Progression in non-bypassed arteries was seen only when symptoms occurred later. Late results in angina pectoris were less favourable in the group undergoing reoperation: 31 (65%) of the 48 operated on twice and 406 (46%) of the 877 patients operated on once still had angina at late follow-up. The same fraction in both groups was improved by operation: 88% versus 89%.
The effect of intracoronary nifedipine on regional and global left ventricular performance, coronary vasomotility, and myocardial oxygen consumption is reported. Left ventricular pressures and volume indices of contractility and relaxation were simultaneously recorded in five patients without coronary artery disease. In these patients, nifedipine in the left main coronary artery not only delayed (+115 ms) anterior wall contraction but also slowed (3.5 vs 1.9 cm/s) and depressed it (-26%), resulting in a depression of global left ventricular ejection. This asynchrony and depression of regional contraction is considered to be responsible for the slowed isovolumic contraction and relaxation of the whole ventricle. In 10 other patients with coronary artery disease, coronary sinus blood flow and myocardial oxygen consumption were measured before and after intracoronary nifedipine. The observed decrease in myocardial oxygen consumption (-28%) depended primarily on a decrease in contractility and left ventricular performance. In a third study group of 12 patients with coronary artery disease, the effects of intracoronary nifedipine on the coronary vasomotility of 40 coronary segments (normal, prestenotic, stenotic, poststenotic) were quantitatively determined. Left ventricular haemodynamics and coronary sinus saturation were monitored while the cineangiograms were recorded before and after nifedipine. Nifedipine provoked vasodilatation of the normal (+10.3%), prestenotic, stenotic (+4 to 30%), and poststenotic (+16.4%) coronary segments, which persisted after the disappearance of its direct effects on the myocardium. This transient regional "cardioplegic" effect of nifedipine, associated with an increase in coronary blood flow, a reduction in myocardial oxygen consumption, and a vasodilatation of the epicardial vessels is likely to be beneficial during temporary coronary occlusion such as occurs in spasm or transluminal angioplasty.
The angiotensin-converting enzyme inhibitor, captopril, was given to 19 patients with severe heart failure. Seven patients had acute myocardial infarction and the remainder had chronic myocardial damage caused by ischaemia or valvular disease. Cardiac filling pressures were raised in all, the pulmonary capillary "wedge" pressure being 17 mmHg or more. Captopril, 50 mg orally, raised stroke volume and cardiac output, and reduced heart rate, cardiac filling pressures, systemic arterial pressure, and the plasma concentrations of aldosterone and noradrenaline. These changes were attended by clinical improvement. Decrements in cardiac filling pressures, systemic arterial pressure, and total peripheral resistance were positively correlated with pretreatment plasma renin. Long-term treatment with captopril was offered to 14 patients. Four patients with severe coronary disease died suddenly after initial clinical improvement. In nine patients haemodynamic measurements were repeated after three months. The results showed sustained effects on cardiac output and filling pressures but there was no loss of body weight. The haemodynamic effects were at least as good as with previous vasodilators. The fall in systemic arterial pressure, however, was greater with captopril. Captopril may become a valuable adjunct to the treatment of acute and chronic heart failure, but more information about its effect on coronary blood flow is required.
The influence of nicotine on the production of prostacyclin was studied in umbilical arteries from newborn infants of mothers who were smokers and those who were non-smokers. Thirteen umbilical cords were obtained from the non-smokers and 10 from the smokers. After their ability to produce prostacyclin was shown, the arteries were perfused during a 20 minute period with nicotine 10-7 mol in Krebs-Henseleit buffer and then again during 20 minutes with pure buffer. Nicotine led to a decline in prostacyclin production in all but one artery. In five of 12 arteries from mothers who did not smoke the production recovered during buffer reperfusion, while in nine of 10 arteries from mothers who smoked, prostacyclin production declined to lower levels and did not increase during 20 minutes buffer reperfusion. It is concluded that nicotine has a direct depressive effect on the prostacyclin production in the vascular wall, which in turn may lead to increased platelet aggregation and thus be a precursor of vascular lesions.