Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

PURPOSE

A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains.

METHODS

T. gondii field isolates were collected from different parts of Europe and assessed by whole genome sequencing (WGS). In comparison to ME49 (a type II reference strain), highly polymorphic regions (HPRs) were identified, showing a considerable number of single nucleotide polymorphisms (SNPs). After confirmation by Sanger sequencing, 18 HPRs were used to design a primer panel for multiplex PCR to establish a multilocus Ion AmpliSeq typing method. Toxoplasma gondii isolates and T. gondii present in clinical samples were typed with the new method. The sensitivity of the method was tested with serially diluted reference DNA samples.

RESULTS

Among type II specimens, the method could differentiate the same number of haplotypes as the reference standard, microsatellite (MS) typing. Passages of the same isolates and specimens originating from abortion outbreaks were identified as identical. In addition, seven different genotypes, two atypical and two recombinant specimens were clearly distinguished from each other by the method. Furthermore, almost all SNPs detected by the Ion AmpliSeq method corresponded to those expected based on WGS. By testing serially diluted DNA samples, the method exhibited a similar analytical sensitivity as MS typing.

CONCLUSION

The new method can distinguish different T. gondii genotypes and detect intra-genotype variability among European type II T. gondii strains. Furthermore, with WGS data additional target regions can be added to the method to potentially increase typing resolution.

Validation of the Benefits of Being a Caregiver Scale (BBCS) - further development of an independent characteristic of informal caregiving

BACKGROUND

Although larger amounts of scientific attention have been directed toward the concept of positive aspects of caregiving (PAC) in recent years, a globally uniform definition and a suitable, scientifically valid questionnaire for all informal caregivers have yet to be developed. On the basis of the questionnaires that already exist for measuring PAC, the authors aimed to (a) concretize the concept and (b) develop a new scale by focusing only on items that show that family caregivers experience a benefit for themselves and that the benefit they experience is the result of their caregiving activities.

METHODS

The Benefits of Being a Caregiver Scale (BBCS) was validated on data from 961 informal caregivers. Cronbach's alpha was calculated to assess the internal consistency of the items, and a factor analysis was conducted to determine the structure of the BBCS. The discriminatory power and item difficulties were examined. Construct validity was established by testing four hypotheses.

RESULTS

The factor analysis confirmed the single-factor structure of the BBCS. Cronbach's alpha for the total scale was 0.922. One of the 15 items did not show good to very good discriminatory power and was excluded from the final version of the scale. A higher BBCS score was observed if the caregiver experienced more positive aspects of caregiving and tended to have better general coping skills and a positive relationship with the care-receiver. The BBCS score was not associated with the subjective burden of the caregiver. Results confirmed the validity of the BBCS.

CONCLUSION

The BBCS is a valid assessment instrument for measuring the benefits that caregivers experience from their caregiving work and can easily be used in research and practice. The BBCS is available free of charge in English and German ( http://www.caregiver-benefits.de ).

Evaluation of an open forecasting challenge to assess skill of West Nile virus neuroinvasive disease prediction

BACKGROUND

West Nile virus (WNV) is the leading cause of mosquito-borne illness in the continental USA. WNV occurrence has high spatiotemporal variation, and current approaches to targeted control of the virus are limited, making forecasting a public health priority. However, little research has been done to compare strengths and weaknesses of WNV disease forecasting approaches on the national scale. We used forecasts submitted to the 2020 WNV Forecasting Challenge, an open challenge organized by the Centers for Disease Control and Prevention, to assess the status of WNV neuroinvasive disease (WNND) prediction and identify avenues for improvement.

METHODS

We performed a multi-model comparative assessment of probabilistic forecasts submitted by 15 teams for annual WNND cases in US counties for 2020 and assessed forecast accuracy, calibration, and discriminatory power. In the evaluation, we included forecasts produced by comparison models of varying complexity as benchmarks of forecast performance. We also used regression analysis to identify modeling approaches and contextual factors that were associated with forecast skill.

RESULTS

Simple models based on historical WNND cases generally scored better than more complex models and combined higher discriminatory power with better calibration of uncertainty. Forecast skill improved across updated forecast submissions submitted during the 2020 season. Among models using additional data, inclusion of climate or human demographic data was associated with higher skill, while inclusion of mosquito or land use data was associated with lower skill. We also identified population size, extreme minimum winter temperature, and interannual variation in WNND cases as county-level characteristics associated with variation in forecast skill.

CONCLUSIONS

Historical WNND cases were strong predictors of future cases with minimal increase in skill achieved by models that included other factors. Although opportunities might exist to specifically improve predictions for areas with large populations and low or high winter temperatures, areas with high case-count variability are intrinsically more difficult to predict. Also, the prediction of outbreaks, which are outliers relative to typical case numbers, remains difficult. Further improvements to prediction could be obtained with improved calibration of forecast uncertainty and access to real-time data streams (e.g. current weather and preliminary human cases).

Evaluating the discriminatory power of the velocity field diagram and timed-up-and-go test in determining the fall status of community-dwelling older adults: a cross-sectional observational study

Background

Systematic reviews demonstrated that gait variables are the most reliable predictors of future falls, yet are rarely included in fall screening tools. Thus, most tools have higher specificity than sensitivity, hence may be misleading/detrimental to care. Therefore, this study aimed to determine the validity, and reliability of the velocity field diagram (VFD -a gait analytical tool), and the Timed-up-and-go test (TUG)-commonly used in Nigeria as fall screening tools, compared to a gold standard (known fallers) among community-dwelling older adults.

Method

This is a cross-sectional observational study of 500 older adults (280 fallers and 220 non-fallers), recruited by convenience sampling technique at community health fora on fall prevention. Participants completed a 7-m distance with the number of steps and time it took determined and used to compute the stride length, stride frequency, and velocity, which regression lines formed the VFD. TUG test was simultaneously conducted to discriminate fallers from non-fallers. The cut-off points for falls were: TUG times ≥ 13.5 s; VFD’s intersection point of the stride frequency, and velocity regression lines (E₁) ≥ 3.5velots. The receiver operating characteristic (ROC) area under the curves (AUC) was used to explore the ability of the E₁ ≥ 3.5velots to discriminate between fallers and non-fallers. The VFD’s and TUG’s sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were determined. Alpha was set at p < 0.05.

Results

The VFD versus TUG sensitivity, specificity, PPV and NPV were 71%, 27%, 55%, and 42%, versus 39%, 59%, 55%, and 43%, respectively. The ROC’s AUC were 0.74(95%CI:0.597,0.882, p = 0.001) for the VFD. The optimal categorizations for discrimination between fallers/non-fallers were ≥ 3.78 versus ≤ 3.78 for VFD (fallers versus non-fallers prevalence is 60.71% versus 95.45%, respectively), with a classification accuracy or prediction rate of 0.76 unlike TUG with AUC = 0.53 (95% CI:0.353,0.700, p = 0.762), and a classification accuracy of 0.68, and optimal characterization of ≥ 12.81 s versus ≤ 12.81 (fallers and non-fallers prevalence = 92.86% versus 36.36%, respectively).

Conclusion

The VFD demonstrated a fair discriminatory power and greater reliability in identifying fallers than the TUG, and therefore, could replace the TUG as a primary tool in screening those at risk of falls.

First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach

BACKGROUND

The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panels by different research groups studying the same population can cause problems and bias in data analysis. A priority issue in conservation genetics is the comparability of data produced by different labs with different methods. Here, we compared data from previous and ongoing studies to identify a panel of microsatellite loci efficient for the long-term monitoring of Apennine brown bears (Ursus arctos marsicanus), aiming at reducing genotyping uncertainty and allowing reliable individual identifications overtimes.

RESULTS

We examined all microsatellite markers used up to now and identified 19 candidate loci. We evaluated the efficacy of 13 of the most commonly used loci analyzing 194 DNA samples belonging to 113 distinct bears selected from the Italian national biobank. We compared data from 4 different marker subsets on the basis of genotyping errors, allelic patterns, observed and expected heterozygosity, discriminatory powers, number of mismatching pairs, and probability of identity. The optimal marker set was selected evaluating the low molecular weight, the high discriminatory power, and the low occurrence of genotyping errors of each primer. We calibrated allele calls and verified matches among genotypes obtained in previous studies using the complete set of 13 STRs (Short Tandem Repeats), analyzing six invasive DNA samples from distinct individuals. Differences in allele-sizing between labs were consistent, showing a substantial overlap of the individual genotyping.

CONCLUSIONS

The proposed marker set comprises 11 Ursus specific markers with the addition of cxx20, the canid-locus less prone to genotyping errors, in order to prevent underestimation (maximizing the discriminatory power) and overestimation (minimizing the genotyping errors) of the number of Apennine brown bears. The selected markers allow saving time and costs with the amplification in multiplex of all loci thanks to the same annealing temperature. Our work optimizes the available resources by identifying a shared panel and a uniform methodology capable of improving comparisons between past and future studies.

A panel of jitter/shimmer may identify functional dysphonia at risk of failure after speech therapy

BACKGROUND

There are no reliable outcome predictors for functional dysphonia (FD) patients.

OBJECTIVES

To investigate if any clinical or phoniatric characteristics could identify FD patients at risk of negative outcome after speech therapy.

METHODS

We retrospectively reviewed the results of 78 FD patients treated with the proprioceptive elastic method. Before and one-month after therapy, patients underwent endoscopy, acoustic analysis with Multi-Dimensional Voice Program, and Voice Handicap Index-10 questionnaire (VHI-10). Negative outcome was the persistence of VHI-10 ≥ 13.

RESULTS

26 FD patients had negative outcome (i.e. VHI-10 ≥ 13) after speech therapy. At univariate analysis, clinical variables (i.e. sex, age, comorbidities, dysphonia duration, and professional voice use) were not associated with the outcome. Elevated Jitter% (Jitt; p = 0.03), Shimmer% (Shim; statistical trend, p = 0.06), and Noise to Harmonics Ratio (statistical trend, p = 0.06) were found in patients with poor results. At multivariate analysis, higher Jitt was an independent negative prognostic factor (p = 0.02), while a statically trend was identified for Shim (p = 0.06). A panel of Jitt >1.5 and Shim >5.1 showed an acceptable discriminatory power (AUC [ROC] = 0.76) according to Hosmer and Lemeshow scale.

CONCLUSION

A panel of two acoustic analysis parameters could help in identifying FD patients at risk of speech therapy failure. Further studies in these patients are needed to evaluate the most efficient treatment protocol.

Introducing the Best Six Loci in Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat (MIRU-VNTR) Typing for Mycobacterium Tuberculosis Genotyping

BACKGROUND

Tuberculosis (TB) still remains endemic worldwide making epidemiological studies essential to mitigating efforts implicated in identifying its source, controlling, and preventing the spread of dangerous strains amongst humans such as Mycobacterium tuberculosis (Mtb).

METHODS

In this study, we sought to determine the 6 Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat (MIRU-VNTR) loci with high discriminatory powers for Mtb genotyping as well as the loci with the highest and the lowest discriminatory powers for MIRU-VNTR. To conduct our search, we used several databases such as science direct, Embase (Elsevier), Web of Science, Scopus and Medline via PubMed. Searches were performed using key words including: Mycobacterium tuberculosis, MIRU-VNTR, Allele diversity, Genetic diversity and human patient. Finally, 56 articles were selected after filtering out titles, abstracts and full texts.

RESULTS

Loci with high discriminatory powers included MIRU10 and MIRU26, while MIRU2, MIRU20, MIRU24 and ETRD had poor discriminatory powers. According to previous data in the literature, the loci MIRU10, MIRU26, MIRU40, QUB 26, QUB 11b and Mtub21 have high discriminatory powers.

CONCLUSION

Therefore, these loci recommended for genotyping Mtb to save time and cost and to ensure the production of reliable results.

Comparison of three molecular subtyping techniques for Listeria monocytogenes

Listeria monocytogenes is a foodborne pathogen. The recent alert for L. monocytogenes in vegetables from Argentina warns about the importance of reinforcing its isolation, characterization and subtyping in food, clinical and environmental samples. The aim of the present study was to compare the discriminatory power of enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR), automated ribotyping and pulsed-field gel electrophoresis (PFGE) to subtype strains of L. monocytogenes isolated from Argentine meat and environmental samples. Simpson's Diversity Index (DI) was calculated on the basis of based on the dendrograms obtained in the by cluster analysis, showing the following discriminatory power: ApaI-PFGE (0.980), AscI-PFGE (0.966), ribotyping (0.912), ERIC-PCR (0.886). The ID values between ApaI- and AscI-PFGE and between ribotyping and ERIC-PCR were not significantly different. Of the three techniques evaluated, PFGE showed the highest discriminatory power. However, the subtyping techniques should be accompanied by effective food monitoring strategies and reliable clinical and epidemiological studies.

A comparative study reveals the higher resolution of RAPD over ARDRA for analyzing diversity of Nostoc strains

Nostoc is a diverse genus of filamentous cyanobacteria with tremendous potential for agricultural and industrial applications. Morphometric methods and routine 16S rDNA-based identification undermines the genetic diversity and impedes strain-level differentiation. A comparative study to deduce the discriminatory power of random amplified polymorphic DNA (RAPD) and amplified ribosomal DNA restriction analysis (ARDRA) for analyzing the genetic diversity of 20 Nostoc strains of diverse geographical origin was carried out. The RAPD primer used in the study generated 100% polymorphic profile. HIP TG primer produced the highest number of bands and fragments. Five primers, viz. OPA 08, OPA 11, HIP GC, OPAH 02 and OPF 05 could produce unique bands for 11 strains. Cluster analysis using the RAPD profile showed 12.5-25% similarity among the strains. Following in silico restriction analysis, two restriction enzymes, viz. HaeIII and HinfI were selected for ARDRA. However, clustering based on the restriction pattern showed 22.5-100% similarity. Results of the present study clearly indicate higher resolution of RAPD which can be reliably used for strain-level differentiation of Nostoc strains.

Genetic Diversity of Arcobacter Species of Animal and Human Origin in Andhra Pradesh, India

Arcobacter is an emerging foodborne pathogen having zoonotic significance. Enterobacterial repetitive intergenic consensus (ERIC) PCR and repetitive sequence-based PCR (rep-PCR) analysis of a total of 41 Arcobacter isolates revealed a greater degree of genetic diversity. ERIC-PCR genotyping distinguished 14, 13 and 12 genotypes among 16, 13 and 12 isolates of A. butzleri, A. cryaerophilus and A. skirrowii, respectively. Rep-PCR genotyping distinguished 15, 12 and 11 genotypes among 16, 13 and 12 isolates of A. butzleri, A. cryaerophilus and A. skirrowii, respectively. The discriminatory power for ERIC and rep-PCR was found to be 0.997 and 0.996, respectively. Close clustering between isolates of animal and human origin are indicative of probable zoonotic significance.

Revisiting the Hunter Gaston discriminatory index: Note of caution and courses of change

Hunter Gaston Discriminatory Index (HGDI) is a widely used estimator of discriminatory power of genotyping methods and diversity of molecular markers in bacterial pathogens, including Mycobacterium tuberculosis. In my opinion, the index is somewhat misleading: a closer look at common practice and particular studies reveals that values in the range of 0.6-0.9 are modest but uncritically perceived as high. I propose and discuss three courses of change: (i) to continue using HGDI but be aware of the true meaning behind its value and increase a threshold of acceptable resolution to the more adequate values of 0.90-0.99, depending on study design; (ii) to turn to other known indices of diversity (e.g., Shannon index), in order to complement HGDI; (iii) to develop new, intuitively more realistic estimator.

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.