A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture

Invasive fungal infections are increasingly common and carry high morbidity and mortality, yet fungal diagnostics lag behind bacterial diagnostics in rapidly identifying the causal pathogen. We previously devised a fluorescent hybridization-based assay to identify bacteria within hours directly from blood culture bottles without subculture, called phylogeny-informed rRNA-based strain identification (Phirst-ID). Here, we adapt this approach to unambiguously identify 11 common pathogenic Candida species, including C. auris, with 100% accuracy from laboratory culture (33 of 33 strains in a reference panel, plus 33 of 33 additional isolates tested in a validation panel). In a pilot study on 62 consecutive positive clinical blood cultures from two hospitals that showed yeast on Gram stain, Candida Phirst-ID matched the clinical laboratory result for 58 of 59 specimens represented in the 11-species reference panel, without misclassifying the 3 off-panel species. It also detected mixed Candida species in 2 of these 62 specimens, including the one discordant classification, that were not identified by standard clinical microbiology workflows; in each case the presence of both species was validated by both clinical and experimental data. Finally, in three specimens that grew both bacteria and yeast, we paired our prior bacterial probeset with this new Candida probeset to detect both pathogen types using Phirst-ID. This simple, robust assay can provide accurate Candida identification within hours directly from blood culture bottles, and the conceptual approach holds promise for pan-microbial identification in a single workflow.

LAY SUMMARY

Candida bloodstream infections cause considerable morbidity and mortality, yet slow diagnostics delay recognition, worsening patient outcomes. We develop and validate a novel molecular approach to accurately identify Candida species directly from blood culture one day faster than standard workflows.

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.

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.