Clinical Pilot of Bacterial Transcriptional Profiling as a Combined Genotypic and Phenotypic Antimicrobial Susceptibility Test.

Antimicrobial resistance is a growing health threat, but standard methods for determining antibiotic susceptibility are slow and can delay optimal treatment, which is especially consequential in severe infections such as bacteremia. Novel approaches for rapid susceptibility profiling have emerged that characterize either bacterial response to antibiotics (phenotype) or detect specific resistance genes (genotype). GoPhAST-R is a novel assay, performed directly on positive blood cultures, that integrates rapid transcriptional response profiling with detection of key resistance gene transcripts, thereby providing simultaneous data on both phenotype and genotype. Here, we performed the first clinical pilot of GoPhAST-R on 42 positive blood cultures: 26 growing Escherichia coli, 15 growing Klebsiella pneumoniae, and 1 with both. An aliquot of each positive blood culture was exposed to 9 different antibiotics, lysed, then underwent rapid transcriptional profiling on the NanoString® platform; results were analyzed using an in-house susceptibility classification algorithm. GoPhAST-R achieved 95% overall agreement with standard antimicrobial susceptibility testing methods, with the highest agreement for beta-lactams (98%) and the lowest for fluoroquinolones (88%). Epidemic resistance genes including the extended spectrum beta-lactamase bla CTX-M-15 and the carbapenemase bla KPC were also detected within the population. This study demonstrates the clinical feasibility of using transcriptional response profiling for rapid resistance determination, although further validation with larger and more diverse bacterial populations will be essential in future work. GoPhAST-R represents a promising new approach for rapid and comprehensive antibiotic susceptibility testing in clinical settings.

Multigene testing of moderate-risk genes: be mindful of the missense.

BACKGROUND: Moderate-risk genes have not been extensively studied, and missense substitutions in them are generally returned to patients as variants of uncertain significance lacking clearly defined risk estimates. The fraction of early-onset breast cancer cases carrying moderate-risk genotypes and quantitative methods for flagging variants for further analysis have not been established. METHODS: We evaluated rare missense substitutions identified from a mutation screen of ATM, CHEK2, MRE11A, RAD50, NBN, RAD51, RINT1, XRCC2 and BARD1 in 1297 cases of early-onset breast cancer and 1121 controls via scores from Align-Grantham Variation Grantham Deviation (GVGD), combined annotation dependent depletion (CADD), multivariate analysis of protein polymorphism (MAPP) and PolyPhen-2. We also evaluated subjects by polygenotype from 18 breast cancer risk SNPs. From these analyses, we estimated the fraction of cases and controls that reach a breast cancer OR≥2.5 threshold. RESULTS: Analysis of mutation screening data from the nine genes revealed that 7.5% of cases and 2.4% of controls were carriers of at least one rare variant with an average OR≥2.5. 2.1% of cases and 1.2% of controls had a polygenotype with an average OR≥2.5. CONCLUSIONS: Among early-onset breast cancer cases, 9.6% had a genotype associated with an increased risk sufficient to affect clinical management recommendations. Over two-thirds of variants conferring this level of risk were rare missense substitutions in moderate-risk genes. Placement in the estimated OR≥2.5 group by at least two of these missense analysis programs should be used to prioritise variants for further study. Panel testing often creates more heat than light; quantitative approaches to variant prioritisation and classification may facilitate more efficient clinical classification of variants.

A systematic review of the role of cardiopulmonary exercise testing in vascular surgery.

OBJECTIVE: To perform a systematic review of cardiopulmonary exercise testing (CPET) in the pre-operative evaluation of patients with abdominal aortic aneurysm or peripheral vascular disease requiring surgery. METHODS: Review methods and reporting were according to the PRISMA guidelines. Studies were eligible if they reported CPET-derived physiological parameters in patients undergoing abdominal aortic aneurysm repair or lower extremity arterial bypass. Data were extracted regarding patient populations and correlation between CPET and surgical outcomes including mortality, morbidity, critical care bed usage and length of hospital stay. RESULTS: The searches identified 1301 articles. Although 53 abstracts referred to the index vascular procedures, only seven articles met inclusion criteria. There were no data from randomised controlled trials. Data from prospective studies did not comprehensively correlate CPET and surgical outcomes in patients with abdominal aortic aneurysms. There were no studies reporting CPET in patients undergoing lower extremity arterial bypass. Major limitations included small sample sizes, lack of blinding, and an absence of reporting standards. CONCLUSION: The paucity of robust data precludes routine adoption of CPET in risk stratifying patients undergoing major vascular surgery. The use of CPET should be restricted to clinical trials and experimental registries, reporting to consensus-defined standards.

A systematic review of percutaneous mechanical thrombectomy in the treatment of deep venous thrombosis.

BACKGROUND: In selected cases of deep vein thrombosis (DVT), catheter-directed thrombolysis (CDT) may be superior to conventional treatment with anticoagulation alone, as it can prevent DVT recurrence and the development of post-thrombotic syndrome (PTS). Percutaneous mechanical thrombectomy (PMT) devices offer a minimally invasive adjunctive strategy and the data on these emerging technologies require review. OBJECTIVES: To review the evidence for PMT devices in DVT in terms of case selection, technical feasibility and procedural outcomes. METHODS: Medline, trial registries, conference proceedings and article reference lists were searched to identify case series reporting PMT device use. Data were extracted for review. RESULTS: 16 retrospective case series have reported the use of rheolytic, rotational, or ultrasound-assisted PMT in a total of 481 patients. No randomised trials were available. Technical success of 82-100% was reported with Grade II or III lysis in 83-100% of patients. The different devices all appeared to be safe, with no reported procedure-related deaths or strokes and <1% incidence of symptomatic PE. Bleeding complications were reported in 6/16 studies, in which 4-14% of patients required transfusion (global incidence 11/146 patients, 7.5%). CONCLUSION: PMT appears feasible and safe, though the level of evidence available is poor. Major RCTs and registry data are required to determine the economic and clinical benefit of various devices used alone or in combination, for differing thrombus characteristics and clinical scenarios. Until these data are available there is little substantial evidence to support the routine use of PMT over CDT alone.

Effects of dietary ingredients and Eimeria acervulina infection on chick performance, apparent metabolizable energy, and amino acid digestibility.

In each of three 2-wk experiments, chicks were inoculated on d 9 or 11 with 5.0 x 10(5) Eimeria acervulina sporulated oocysts (acute infection) or on d 9, 12, 15, and 18 with 1.5 x 10(5) sporulated oocysts (chronic infection). In Experiment 1, both fish meal (15%) and GroBiotic-P (GB; International Ingredient Corporation, St. Louis, MO; 5%) diets completely ameliorated the negative effects of acute and chronic coccidiosis infection on growth performance of crossbred chicks. The acute coccidiosis infection greatly reduced MEn and amino acid (AA) digestibility, and the magnitude of response varied with the timing of excreta collection after inoculation. Both fish meal and GB diets ameliorated the large negative effects of coccidiosis infection on MEn and AA digestibility. In Experiment 2, a wheat-barley-pectin diet and acute coccidiosis infection depressed crossbred chick BW gain, AA digestibility, and MEn in comparison with a corn-soybean meal diet; there generally were no interactions between diet type and coccidiosis infection. In Experiment 3, using commercial broiler chicks, diets containing 2 to 6% GB did not improve the growth performance of coccidiosis-infected chicks, but they did improve the growth of the noninfected chicks. The results of this study indicate that coccidiosis infection (E. acervulina) reduces MEn and AA digestibility in chicks and that the coccidiosis effect is influenced by diet composition, type of infection (acute vs. chronic), and timing of excreta collection.

Evaluation of a rapid, new method for detecting serum IgG antibodies to Helicobacter pylori.

There is an increased need for rapid, inexpensive tests to diagnose Helicobacter pylori infection. Our objective was to determine the performance characteristics of an immunochromatographic test (ICT) for detection of anti-H. pylori IgG antibodies. A commercially available ICT kit (FlexSure HP) was tested with a well-characterized cohort of banked sera as well as with fresh serum from randomly selected symptomatic patients. The ICT was evaluated with 107 stored sera and 96 prospective patients. The test correctly identified 65 of 68 H. pylori-infected and 37 of 39 noninfected stored sera and 54 of 57 infected and 30 of 39 noninfected patients. Sensitivity, specificity, and positive and negative predictive values were 96%, 95%, 97%, and 93% in stored serum and 95%, 77%, 86%, and 91% in fresh serum, respectively. We concluded that the ICT, reported at 4 min, is highly sensitive for detecting anti-H. pylori IgG antibodies in human serum. With a high negative predictive value, the test may be used to exclude H. pylori infection in symptomatic patients.

Prospective evaluation of a new urea-membrane test for the detection of Helicobacter pylori in gastric antral tissue.

AIM: To determine the sensitivity, specificity, and positive and negative predictive values of a newly developed urea-membrane test for the detection of Helicobacter pylori in gastric tissue. METHODS: Patients presenting for upper endoscopy with no recent exposure to H. pylori-altering drugs were enrolled. Antral biopsy specimens were tested by the urea-membrane and urea-gel methods and submitted for histology. Patients underwent [13C]urea breath tests. Presence of H. pylori was established by histology or the combination of a positive [13C]urea breath test and a positive urea-gel test. Absence of H.pylori required both the [13C]urea breath test and the invasive tests to be negative. The urea-membrane test was reported at 1 hour. RESULTS: Ninety-nine patients (47 men and 52 women) with a mean age of 51.43 +/- 14.9 years participated. Fifty of 99 patients (prevalence, 50.5%) tested positive for H. pylori. The urea-membrane test correctly identified 49 of 50 H. pylori-positive and 46 of 49 H. pylori-negative patients, yielding sensitivity, specificity, and positive and negative predictive values of 98.0%, 93.9%, and 94.2% and 97.9%, respectively, in this population. CONCLUSIONS: Rapidly available and reliable results from the urea-membrane test can facilitate clinical decision prior to patient discharge from the endoscopy suite.

Instance-based clusters of fear and anxiety: is ambiguity an essential dimension?

Students rated instances of fear-like emotions on 34 attributes related to distinctions between fear and anxiety in the literature, and then on relative degree of fear vs anxiety produced. Instances rated most fear-like had been rated as higher than more anxiety-like instances in terms of clarity and reality of causes, but lower in terms of the clarity of understanding the situation and knowing what to do when in it. There were two distinct clusters of fear-like instances and two distinct "anxiety clusters;" the two fear clusters were more different from each other than from the two anxiety clusters in terms of ratings on these clarity-related attributes. Analysis suggested (a) that "pure fear" is less vague than anxiety in some ways but more vague in other ways and (b) that comparisons have to be qualified because emotion-labels usually encompass more than one kind of emotion. However, differences in present-centeredness and other factors may be reliable and general.