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Carbapenem resistant (CRE) and carbapenemase producing Enterobacterales (CPE) in particular, represent a major threat for healthcare systems worldwide. Rapid, reliable, and easy to perform assays are required to enable targeted and effective therapy. MALDI-TOF MS based carbapenemase diagnostics has potential advantages over molecular and phenotypic sensitivity tests, especially in terms of time to result. So far, only one mass spectrometry (MS)-based carbapenemase test system is commercially available for routine use. The aim of this study was to compare the performance of the established system to a novel MS-based test to identify CPE isolates. Forty consecutive CRE isolates (70% CPEs) were pre-screened for carbapenemase activity by routine laboratory methods. Isolates then were tested using the to date only IVD CE certified MALDI-TOF MS carbapenemase detection assay (MBT STAR-Carba IVD Kit; Bruker Daltonics) and a novel test designed for the recently launched EXS2600 MALDI-TOF MS system (Carbapenemase Activity Kit; Zybio). Valid results were obtained for 93% and 85% isolates by the Bruker and the Zybio assay, respectively. Sensitivities, specificities, positive and negative predictive values were 92%, 91%, 96%, and 83% for the Bruker assay and 96%, 64%, 85%, and 88% for the Zybio assay. There are notable differences concerning the handling of the assays. In summary, both systems featured high sensitivities for the detection of carbapenemases, but the Bruker assay yielded less false-positive results. There are advantages and disadvantages concerning the handling for each system, but both proved to be suitable for the use in a routine laboratory. [ABSTRACT FROM AUTHOR]

The widespread spread of bacterial antimicrobial resistance (AMR) and multidrug-resistant bacteria poses a significant threat to global public health. Traditional methods for detecting bacterial AMR are simple, reproducible, and intuitive, requiring long time incubation and high labor intensity. To quickly identify and detect bacterial AMR is urgent for clinical treatment to reduce mortality rate, and many new methods and technologies were required to be developed. This review summarizes the current phenotypic and genotypic detection methods for bacterial AMR. Phenotypic detection methods mainly include antimicrobial susceptibility tests, while genotypic detection methods have higher sensitivity and specificity and can detect known or even unknown drug resistance genes. However, most of the current tests are either genotypic or phenotypic and rarely combined. Combining the advantages of phenotypic and genotypic methods, combined with the joint application of multiple rapid detection methods may be the trend for future AMR testing. Driven by rapid diagnostic technology, big data analysis, and artificial intelligence, detection methods of bacterial AMR are expected to constantly develop and innovate. Adopting rational detection methods and scientific data analysis can better address the challenges of bacterial AMR and ensure human health and social well-being. [ABSTRACT FROM AUTHOR]

Abstract Carbapenem resistant (CRE) and carbapenemase producing Enterobacterales (CPE) in particular, represent a major threat for healthcare systems worldwide. Rapid, reliable, and easy to perform assays are required to enable targeted and effective therapy. MALDI-TOF MS based carbapenemase diagnostics has potential advantages over molecular and phenotypic sensitivity tests, especially in terms of time to result. So far, only one mass spectrometry (MS)-based carbapenemase test system is commercially available for routine use. The aim of this study was to compare the performance of the established system to a novel MS-based test to identify CPE isolates. Forty consecutive CRE isolates (70% CPEs) were pre-screened for carbapenemase activity by routine laboratory methods. Isolates then were tested using the to date only IVD CE certified MALDI-TOF MS carbapenemase detection assay (MBT STAR-Carba IVD Kit; Bruker Daltonics) and a novel test designed for the recently launched EXS2600 MALDI-TOF MS system (Carbapenemase Activity Kit; Zybio). Valid results were obtained for 93% and 85% isolates by the Bruker and the Zybio assay, respectively. Sensitivities, specificities, positive and negative predictive values were 92%, 91%, 96%, and 83% for the Bruker assay and 96%, 64%, 85%, and 88% for the Zybio assay. There are notable differences concerning the handling of the assays. In summary, both systems featured high sensitivities for the detection of carbapenemases, but the Bruker assay yielded less false-positive results. There are advantages and disadvantages concerning the handling for each system, but both proved to be suitable for the use in a routine laboratory.

Resistance to multiple antiretroviral drugs among people living with HIV (PLWH) can result in a high pill burden, causing toxicity and drug interactions. Thus, the goal is to simplify treatment regimens while maintaining effectiveness. However, former resistance analysis data may not be current or complete. The use of proviral DNA genotyping may assist in selecting appropriate treatment options. A retrospective study was carried out on individuals belonging to the Cologne HIV cohort with a resistance history to two or more antiretroviral (ARV) classes and on non-standard antiretroviral therapy (ART). Patients required former viral RNA and a recent proviral DNA resistance test to be available prior to the switch to ART. Potential discrepancies between resistance test results obtained through RNA and proviral DNA methods and the consequent virological and clinical outcomes following ART adjustments were analyzed. Out of 1250 patients, 35 were eligible for inclusion in this study. The median length of known HIV infection was 27 years, and the median duration of ART was 22 years. Of the 35 participants, 16 had received all five ARV classes. Based on proviral DNA genotyping results, ART was simplified in 17 patients. At the last follow-up examination after changing therapy, 15 patients had HIV RNA <50 copies/mL (median 202 days, range 21–636). The mean number of pills per day decreased from eight to three, and the median intake frequency decreased from two to one time/day (ranges 1–2). Our study supports the use of proviral DNA genotyping as a safe strategy for switching to simplified ART regimens. However, the lack of extensive research on the advantages of proviral DNA genotyping makes it challenging to fully assess its benefits in terms of treatment selection. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the 9-month cost and health-related quality of life (HRQOL) outcomes of resistance versus viral load testing strategies to manage virological failure in low-middle income countries. We analyzed secondary outcomes from the REVAMP clinical trial: a pragmatic, open label, parallel-arm randomized trial investigating resistance versus viral load testing for individuals failing first-line treatment in South Africa and Uganda. We collected resource data, valued according to local cost data and used the 3-level version of EQ-5D to measure HRQOL at baseline and 9 months. We applied seemingly unrelated regression equations to account for the correlation between cost and HRQOL. We conducted intention-to-treat analyses with multiple imputation using chained equations for missing data and performed sensitivity analyses using complete cases. For South Africa, resistance testing and opportunistic infections were associated with statistically significantly higher total costs, and virological suppression was associated with lower total cost. Higher baseline utility, higher cluster of differentiation 4 (CD4) count, and virological suppression were associated with better HRQOL. For Uganda, resistance testing and switching to second-line treatment were associated with higher total cost, and higher CD4 was associated with lower total cost. Higher baseline utility, higher CD4 count, and virological suppression were associated with better HRQOL. Sensitivity analyses of the complete-case analysis confirmed the overall results. Resistance testing showed no cost or HRQOL advantage in South Africa or Uganda over the 9-month REVAMP clinical trial. • We analyzed cost and health-related quality of life (HRQOL) data using seemingly unrelated regression equations to account for joint correlation: this method is not widely published. • We undertook analysis in the context of a marginal, nonsignificant benefit in clinical primary outcome, proceeding based on strong economic hypotheses suggesting cost and HRQOL benefits for resistance testing. • Our study benefits from rich, primary, individual patient-level data to compare baseline and 9-month cost and HRQOL. • Notably, in contrast to high-income countries, resistance testing showed no 9-month cost or HRQOL advantage compared with viral load testing in low-middle income countries. • Results are key to informing multinational partners, nongovernment organizations, and public health policy makers about the use of resistance testing in clinical practice. • They are also important for informing the lifetime cost-effectiveness analysis of resistance testing in the era of new resistance testing methods and treatment regimens. [ABSTRACT FROM AUTHOR]

Resistance to multiple antiretroviral drugs among people living with HIV (PLWH) can result in a high pill burden, causing toxicity and drug interactions. Thus, the goal is to simplify treatment regimens while maintaining effectiveness. However, former resistance analysis data may not be current or complete. The use of proviral DNA genotyping may assist in selecting appropriate treatment options. A retrospective study was carried out on individuals belonging to the Cologne HIV cohort with a resistance history to two or more antiretroviral (ARV) classes and on non-standard antiretroviral therapy (ART). Patients required former viral RNA and a recent proviral DNA resistance test to be available prior to the switch to ART. Potential discrepancies between resistance test results obtained through RNA and proviral DNA methods and the consequent virological and clinical outcomes following ART adjustments were analyzed. Out of 1250 patients, 35 were eligible for inclusion in this study. The median length of known HIV infection was 27 years, and the median duration of ART was 22 years. Of the 35 participants, 16 had received all five ARV classes. Based on proviral DNA genotyping results, ART was simplified in 17 patients. At the last follow-up examination after changing therapy, 15 patients had HIV RNA

Simple Summary: Different isolates of Cydia pomonella granulovirus (CpGV) have been formulated into different biological control agents that are applied to reduce the infestation and losses induced by codling moth in organic and integrated apple and pear orchards. Cyd-X® is the most widely applied CpGV product in apple orchards in the USA and contains a single active ingredient, the isolate CpGV-M (GV-0001). Aiming to investigate the susceptibility of codling moth to GV-0001, we used a discriminating virus concentration to screen five codling moth populations derived from Washington State (USA), which were reared in the laboratory (colony WA1-WA5). The results indicate that colony WA3 had a significantly reduced susceptibility to GV-0001 and survivors from the bioassay can produce offspring. WA3 represents the first documented case of CpGV resistance in the USA. In further tests, WA3 showed resistance to all commercial CpGV agents currently registered in the USA. Nonetheless, the resistant WA3 colony showed high susceptibility to three newly developed CpGV preparations. Therefore, the introduction of the novel CpGV formulations may allow the maintenance of sustainable management programs for codling moth in the USA. Codling moth (Cydia pomonella L.) is a very important pest in apple, pear, and walnut orchards worldwide, including the USA. Cydia pomonella granulovirus (CpGV) is used to control codling moth in organic and conventional production. Due to increasing codling moth infestations from organic apple orchards in Washington State, USA, five codling moth colonies (WA1-WA5) were screened for their susceptibility relative to the isolate GV-0001, the main active ingredient of Cyd-X®, using a discriminating concentration of 6 × 104 OB/mL. Compared to a susceptible laboratory colony, the observed results indicated that GV-0001 lacked efficacy against codling moth colony WA3. It was confirmed that WA3 was the first case of codling moth resistance to CpGV in the USA. Further testing of WA3 was performed on a range of CpGV isolates and a lack of efficacy was observed against additional isolates. However, three newly developed CpGV preparations can efficiently infect larvae from the resistant colony WA3. Our results suggest that there is an urgent need to monitor the situation in the USA, aiming to prevent the emergence or spread of additional codling moth populations with CpGV resistance. Strategies to sustain the efficacy of codling moth control using novel CpGV formulations need to be developed. [ABSTRACT FROM AUTHOR]

We sought to evaluate clinically a hepatitis C virus (HCV) whole-genome, next-generation sequencing (NGS) pipeline that is agnostic to viral genotype. Performance of the NGS pipeline was assessed through comparison of results with Sanger sequencing (SS) of partial HCV genomes. There was 98.7% (376/381) concordance for viral subtype between SS and NGS. The positive and negative per cent agreements for determination of resistance-associated substitutions were 97.8% (95% CI 92.5–99.4%) and 99.9% (95% CI 99.5–100.0%), respectively. The NGS pipeline was also able to detect novel subtypes, mixtures, recombinants, transiently occurring resistance mutations and distinguish re-infection with the same subtype from relapse. Particular scenarios where NGS may be used include settings without universal access to pan-genotypic antiviral regimens, those infected with a 'rare' subtype or who have been failed by first-line therapy, and in cases of suspected re-infection. [ABSTRACT FROM AUTHOR]

Codling moth (Cydia pomonella L.) is a very important pest in apple, pear, and walnut orchards worldwide, including the USA. Cydia pomonella granulovirus (CpGV) is used to control codling moth in organic and conventional production. Due to increasing codling moth infestations from organic apple orchards in Washington State, USA, five codling moth colonies (WA1-WA5) were screened for their susceptibility relative to the isolate GV-0001, the main active ingredient of Cyd-X®, using a discriminating concentration of 6 × 104 OB/mL. Compared to a susceptible laboratory colony, the observed results indicated that GV-0001 lacked efficacy against codling moth colony WA3. It was confirmed that WA3 was the first case of codling moth resistance to CpGV in the USA. Further testing of WA3 was performed on a range of CpGV isolates and a lack of efficacy was observed against additional isolates. However, three newly developed CpGV preparations can efficiently infect larvae from the resistant colony WA3. Our results suggest that there is an urgent need to monitor the situation in the USA, aiming to prevent the emergence or spread of additional codling moth populations with CpGV resistance. Strategies to sustain the efficacy of codling moth control using novel CpGV formulations need to be developed.

Despite the initial success of HIV/AIDS policy, an increasing number of patients are failing the first-line antiretroviral therapy (ART) each year and the failure rates are increasing. There is a need for identification of novel strategies to reduce failure rates. The aims of the study are (1) to design a novel strategy to reduce ART failure rates and (2) to create a stochastic model using Monte Carlo (MC) simulation comparing the novel strategy with existing strategy. A novel strategy based on annual plasma viral load testing and resistance testing for HIV treatment at baseline and at the time of failure was designed. A cohort of 1000 patients each was created for the existing strategy and a novel strategy. Assumptions were included from Indian studies and own data. The two strategies were compared over 20 years of follow-up using stochastic modeling and MC simulation was done for death rates, failure rates, and cost-effectiveness analysis. SimVoi add-in software for MS Excel was used for simulations. Student's t-tests were performed for comparing continuous variables, and the cumulative rates for various outcomes were plotted using Kaplan–Meier analysis. The novel strategy resulted in lower mortality over a 20-year period (279.9 + 7.13 deaths vs 130.43 + 6.03 deaths) with incremental cost per life saved at Rs 32,925 per year. Incremental cost-effectiveness ratio cost per quality-adjusted life year was Rs 1.33 lakhs/annum at constant rate of discounting and just under Rs 90,000 per annum using differential discounting. Armed Forces are likely to benefit by adopting the novel strategy that is cost-effective with a significant mortality benefit. [ABSTRACT FROM AUTHOR]

Summary: The knowledge on molecular alterations in lung cancer have increased during the last decade considerably. Almost every year new genes were detected being targetable, and drugs have been developed and provided for those patients being diagnosed with such a lung cancer. Therefore, it was necessary to update previous recommendations to facilitate a uniform handling for the diagnosis and molecular tests of lung cancer specimen all over Austria. Originally mutation of the epidermal growth factor receptor (EGFR) was the only actionable molecular alteration, now there are more than 10 driver mutations known, and more are detected, and clinical studies are performed. In addition, the technique to test for these mutations have improved, next generation sequencing has opened the option to test several genes in one test. Immuno-oncology has entered the field, and besides the checkpoint death receptor and ligand molecules PD-1/PD-L1 more molecules have been detected and are also tested in clinical studies. To provide equal opportunities to our patients the tests have to be implemented in all pathological institutes involved in lung cancer management. Because pathologists as part of the tumor board have to explain the diagnosis and the molecular alterations and suggest possible treatment options, the tests should be performed in-house, which will provide the optimal quality control. [ABSTRACT FROM AUTHOR]

The treatment of hepatitis C virus (HCV) infection has been revolutionised by the advent of oral, well-tolerated, direct acting antiviral therapies (DAA), with high cure rates. However, in some scenarios, HCV resistance to antiviral therapies may have an impact on treatment success. Public Health England's HCV Resistance Group was established to support clinicians treating people with HCV, where the issue of resistance may be a factor in clinical decision-making, and this review includes the Group's current recommendations on the use of HCV resistance testing. The authors describe the principles behind and approach to HCV resistance testing and consider evidence from in vitro studies, clinical trials and real world cohorts on the impact of HCV resistance on treatment outcomes for particular DAA regimens. Five scenarios are identified in the UK and similar settings, where, in the Group's opinion, resistance testing should be performed. [ABSTRACT FROM AUTHOR]

• We provide recommendations on how to use resistance data and achieve 90% sustained virological response. • If no NS5A resistance-associated substitution is found at failure, choose SOF+NS5A inhibitor with ribavirin. • If genotype 3 and only Y93H, choose SOF+velpatasvir+ribavirin for 24 weeks. • If both NS5A and NS3 resistance-associated substitutions, re-treat with a SOF-based 3-drug regimen+ribavirin. • Our data may be relevant for countries with limited access to new direct-acting antiviral combinations. Most hepatitis C virus (HCV)-infected patients failing NS5A inhibitors develop resistance-associated substitutions (RASs). Here we report the use of resistance-guided retreatment of patients who failed prior NS5A inhibitor-containing regimens in the GEHEP-004 cohort. This is the largest direct-acting antiviral (DAA)-resistance cohort study conducted in Spain. We aim to provide indications on how to use resistance information in settings where sofosbuvir/velpatasvir/voxilaprevir may not be available. GEHEP-004 is a prospective multicenter cohort enrolling HCV-infected patients treated with interferon (IFN)-free DAA regimens. Prior to retreatment, population-based sequencing of HCV NS3, NS5A and NS5B genes was performed. After receiving a comprehensive resistance interpretation report, the retreatment regimen was chosen and the sustained virological response (SVR) at 12 weeks after treatment completion (SVR12) was recorded. A total of 342 patients experiencing virological failure after treatment with sofosbuvir/ledipasvir±ribavirin (54%), sofosbuvir/daclatasvir±ribavirin (23%), or paritaprevir-ritonavir/ombitasvir±dasabuvir±ribavirin (20%) were studied. After a resistance report, 186 patients were retreated. An SVR12 was achieved for 88.1% of the patients who failed after sofosbuvir/ledipasvir±ribavirin, 83.3% of the patients who failed after sofosbuvir/daclatasvir±ribavirin, 93.7% of the patients who failed after paritaprevir-ritonavir+ombitasvir±dasabuvir±ribavirin. In our study, we show how resistance-guided retreatment in conjunction with an interpreted report allows patients to achieve SVR rates close to 90%. We hypothesize that SVR rates may even be improved if resistance data are discussed between experienced virologists and treating clinicians. We believe that our data may be relevant for countries where the access to new DAA combination regimens is limited. Hepatitis C infection can be cured with currently available antiviral agents. Only a small proportion of patients experience treatment failure, however, in absolute numbers, a high number of patients may require retreatment. Highly effective combinations of antivirals are also available for retreatment. However, these antivirals might not be available in resource-limited settings. Herein, we show how, by analyzing the cause of resistance, retreatment efficacy with old drugs can get very close to the efficacy of new drug combinations. [ABSTRACT FROM AUTHOR]

Clostridium (Clostridioides) difficile is the main cause of nosocomial diarrhoea. Ribotype 018 (RT018) has been recognized as the predominant strain responsible for C. difficile infection (CDI) in Italy, whereas in most other European countries only sporadic RT018 cases occur. Between August and October 2015, a suspected C. difficile outbreak at two associated hospitals in Southern Germany was investigated by comprehensive molecular typing. Surprisingly, RT018 was detected in 9/82 CDI patients, which has never been described before in a German outbreak. Phenotypic analysis revealed fluoroquinolone and macrolide resistance. Genetic subtyping using multiple-locus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS) was performed and outbreak isolates were directly compared to sporadic German RT018 isolates and to epidemic ones from Milan, Northern Italy. Molecular typing confirmed a hospital outbreak with closely related RT018 isolates. Both, MLVA and WGS revealed high similarity of outbreak strains with epidemic isolates from Italy, but low similarity to other German isolates. Comparison between both typing strategies showed that ribotyping in combination with MLVA was appropriate to identify related isolates and clonal complexes, whereas WGS provided a better discrimination with more detailed information about the phylogenetic relationship of isolates. This is the first hospital outbreak in Germany presumably caused by cross-national transmission of an Italian epidemic RT018 strain. [ABSTRACT FROM AUTHOR]

Highlights • Determination of the HCV genotype is still recommended before initiating HCV therapy. • Resistance-associated substitutions (RAS) in NS5A can limit the efficacy of therapy. • A pan-genotypic NS5A amplification protocol was established. • It successfully amplified 98.1% of GT1–7 samples including samples <1000 IU/ml. • Genotyping by NS5A is reliable and simultaneously allows resistance testing. Abstract Background Chronic infection with the Hepatitis C Virus (HCV) is associated with the risk of progressive liver disease. Although, HCV treatment options and viral cure rates have tremendously increased over the last decade, all currently licensed combination therapies contain inhibitors of the replication complex NS5A. Resistance-associated substitutions (RAS) in NS5A can limit the efficacy of therapy; however, resistance testing is routinely not recommended for all patients. Notably, pan-genotypic combinations have been approved, however the correct identification of the HCV genotype is still required for treatment decisions and is a good predictor for treatment success. Objective The aim of this study was the establishment of a pan-genotypic NS5A amplification method for reliable genotyping and simultaneous resistance testing in a fast and cheap routine diagnostic setup. Study design Pan-genotypic degenerated nested PCR primer were designed and tested in 262 HCV-patients. The collection included samples from genotypes 1–7 and the median viral load was 1.07 × 106 IU/ml (range 248-21 × 106 IU/ml). Results Amplification of the expected 747bp fragment was successful in 257 of 262 (98.1%) samples including samples <1000 IU/ml. The direct comparison of the genotype information obtained with core sequencing to those obtained by NS5A prediction showed high concordance (97.3%) and discrepancies occurred only for relatively rare subtypes. Resistance analysis using Geno2Pheno [HCV] showed NS5A-RAS in 23 of 257 (8.9%) of samples. Conclusions We successfully developed a routine diagnostic method for pan-genotypic amplification of NS5A. This amplicon can be used for simultaneous genotyping and resistance testing for enhancing and improving routine HCV diagnostic. [ABSTRACT FROM AUTHOR]

The black salt marsh mosquito, Aedes taeniorhynchus, is the primary nuisance mosquito in the coastal regions of Florida. This study aimed to establish the baseline susceptibility of Ae. taeniorhynchus to adulticide products used for mosquito control by the Collier Mosquito Control District (CMCD). The Centers for Disease Control and Prevention bottle bioassay was used to test technical-grade and formulated products, and Merus 3.0® was evaluated in semifield cage trials through aerial applications. The results revealed the baseline susceptibility of Ae. taeniorhynchus to the tested materials and the effectiveness of Merus 3.0 to effectively control the Ae. taeniorhynchus. The study provides important information for the development of an integrated mosquito management strategy for controlling Ae. taeniorhynchus mosquito populations in southwest Florida., (Copyright © 2023 by The American Mosquito Control Association, Inc.)

Second-line therapy randomized trials with lopinavir/ritonavir question the value of resistance testing to guide nucleoside reverse transcriptase inhibitor (NRTI) selection. In this study, we investigated the association between baseline drug resistance and treatment outcome after 104 weeks of second-line therapy with NRTIs and either darunavir/ritonavir or lopinavir/ritonavir in West-central Africa. We did an observational analysis of data from 387 individuals in a randomized, open-label 2LADY trial in Burkina Faso, Cameroon, and Senegal. We modeled the association between RTI drug resistance mutations (DRMs) and virological failure (VF) (viral load [VL] <50 copies/mL) at week 104 using logistic regressions. Covariates included baseline VL and CD4+ count, demographic, and adherence data. Overall, 193 (49.9%), 150 (38.8%), and 44 (11.4%) individuals had, respectively, low/none (genotypic susceptibility score [GSS] <1), intermediate (GSS = 1), and high predicted NRTI activity (GSS >1) in their prescribed second-line regimen. The average number of DRMs by drug class, the proportion of individuals by GSS category, and the duration of first-line therapy were not associated with VF (p > .05). High VL at switch was the only consistent prognostic factor for VF after multivariate adjustment (p < .01). Suboptimal adherence, high predicted RTI activity, or low NRTI mutations were associated with VF (p < .05) when using higher end points for VF or in the intention-to-treat analysis. In conclusion, the use of RTIs with predicted reduced activity does not impair second-line protease inhibitor-based therapy. Therefore, HIV care in resource-limited settings should prioritize strategies to improve adherence and targeted VL testing over drug resistance testing for selecting NRTIs during a protease-based second-line switch. [ABSTRACT FROM AUTHOR]

Wheat is affected by many diseases, in Germany eight fungal diseases are recorded during the cultivar registration process. For a commercially successful cultivar, therefore, at least moderate resistances to important diseases, like yellow rust (YR) and Fusarium head blight (FHB), are necessary. Additionally, in 2013 a regional stem rust (SR) epidemic occurred in Central Germany for the first time for decades. Our objective was to analyze the resistance of 36 commercially grown winter wheat cultivars to YR, FHB, and SR in three individual and one combined inoculation. Appreciable disease severities were achieved for YR and FHB at three to four locations in two years (= seven location × year combinations), for SR at one to two locations in two years (= three location × year combinations). Wheat cultivars showed a significant genotypic variation for all diseases with high heritabilities (0.90-0.95). Interaction between inoculation treatments (individual vs. combined) and wheat genotype was not significant for each of the three diseases. Accordingly, correlations between both inoculation treatments were very high (R2 = 0.95-0.99). Several cultivars showed multi-disease resistance (MDR) to YR, FHB, and SR. In conclusion, resistance ranking among genotypes was not changed when plants were challenged with all three pathogens together compared to factorial inoculations of only one of them. Substituting factorial inoculation trials by multi-pathogen inoculation makes it more efficient to select for MDR in practical breeding programs. [ABSTRACT FROM AUTHOR]

This study aims to analyse the emerging global trends and socio-economic benefits of the standardization and accreditation of the burglary-resistance testing of security hardware by manufacturers. The 30 countries that are sampled in this study include 26 EU countries as well as the US, South Korea, Japan and Australia. The major findings of this analysis indicate that the 'standardization and accreditation' trend at the international, regional and national levels in these countries is on the rise, as evidenced by significant increases in domestic and commercial building laws and regulations that aim to enhance security hardware resistance against burglary attacks. It was discovered in this study that despite a number of minor definition disparities, most countries' standards, measurements and rules are relatively consistent in the burglary-resistance tests conducted on security hardware products. Importantly, studies in several countries also showed that a prudent, coordinated, national crime-prevention and security effort can often obtain net gains by not generating any obvious displacement, significantly reducing the costs associated with crime and enhancing awareness of security and safety for users of the built environment. When the significant economic and sociological benefits of the standardization of the burglary-resistance testing of security hardware are fully recognized, it is expected that this trend will not only continue but will likely grow exponentially on a global scale. [ABSTRACT FROM AUTHOR]

The Department of Health and Human Services recommends drug resistance testing at linkage to HIV care. Because receipt and timing of testing are not well characterized, we examined testing patterns among persons with diagnosed HIV who are linked to care. Using surveillance data in six jurisdictions for persons aged ≥13 years with HIV infection diagnosed in 2013, we assessed the proportion receiving testing, and among these, the proportion receiving testing at linkage. Multivariable log-binomial regression modeling estimated associations between selected characteristics and receipt of testing (1) overall, and (2) at linkage among those tested. Of 9,408 persons linked to care, 66% received resistance testing, among whom 68% received testing at linkage. Less testing was observed among male persons who inject drugs (PWID), compared with men who have sex with men (adjusted prevalence ratio [aPR]: 0.88; 95% confidence interval [CI]: 0.81–0.97) and persons living in areas with population <500,000 compared with those in areas with population ≥2,500,000 (aPR: 0.88; CI: 0.84–0.93). In certain jurisdictions, testing was lower for persons with initial CD4 counts ≥500 cells/mm3, compared with those with CD4 counts <200 cells/mm3(aPR range: 0.80–0.85). Of those tested, testing at linkage was lower among male PWID (aPR: 0.85; CI: 0.75–0.95) and, in some jurisdictions, persons with CD4 counts ≥500 cells/mm3(aPR range: 0.63–0.73). Two-thirds of persons with diagnosed HIV who were linked to care received resistance testing, and most received testing at linkage as recommended. Improving receipt and timing of testing among male PWID, persons in less populous settings, and in all jurisdictions, regardless of CD4 count, may improve care outcomes. [ABSTRACT FROM AUTHOR]

The use of Cydia pomonella granulovirus (CpGV) isolates as biological control agents of codling moth (CM) larvae is important in organic and integrated pome fruit production worldwide. The commercially available isolates CpGV-0006, CpGV-R5, and CpGV-V15 have been selected for the control of CpGV resistant CM populations in Europe. In infection experiments, CpGV-0006 and CpGV-R5 were able to break type I resistance and to a lower extent also type III resistance, whereas CpGV-V15 overcame type I and the rarely occurring type II and type III resistance. The genetic background of the three isolates was investigated with next generation sequencing (NGS) tools by comparing their nucleotide compositions to whole genome alignments of five CpGV isolates representing the known genetic diversity of the CpGV genome groups A to E. Based on the distribution of single nucleotide polymorphisms (SNPs) in Illumina sequencing reads, we found that the two isolates CpGV-0006 and CpGV-R5 have highly similar genome group compositions, consisting of about two thirds of the CpGV genome group E and one third of genome group A. In contrast, CpGV-V15 is composed of equal parts of CpGV genome group B and E. According to the identified genetic composition of these isolates, their efficacy towards different resistance types can be explained and predictions on the success of resistance management strategies in resistant CM populations can be made. [ABSTRACT FROM AUTHOR]

Background HCV treatment options and cure rates have tremendously increased in the last decade. Although a pan-genotype HCV treatment has recently been approved, most DAA therapies are still genotype specific. Resistance-associated variants (RAVs) can limit the efficacy of DAA therapy and are associated with increased risk for therapy failure. With the approval of DAA regimens that recommend resistance testing prior to therapy, correct assessment of the genotype and testing for viruses with RAVs is clinically relevant. However, genotyping and resistance testing is generally done in costly and laborious separate reactions. Objective The aim of the study was to establish a genotype-independent full-genome reverse transcription protocol to generate a template for both genotyping and resistance testing and to implement it into our routine diagnostic setup. Study design The complete HCV genome was reverse transcribed with a pan-genotype primer binding at the 3′end of the viral RNA. This cDNA served as template for transcription of the genotyping amplicon in the core region as well as for the resistance testing of NS3, NS5A, and NS5B. Results With the established RT-protocol the HCV core region was successfully amplified and genotyped from 124 out of 125 (99.2%) HCV-positive samples. The amplification efficiency of RAV containing regions in NS3, NS5A, NS5B was 96.2%, 96.6% and 94.4%, respectively. Conclusions We developed a method for HCV full-genome cDNA synthesis and implemented it into a routine diagnostic setup. This cDNA can be used as template for genotyping amplicons covering the core or NS5B region as well as for resistance testing amplicons in NS3, NS5A and NS5B. [ABSTRACT FROM AUTHOR]

Since the first description of Wohlfahrtiimonas chitiniclastica in 2008, a number of well described case reports demonstrating its pathogenic role in humans have been published. Infections may be closely linked to flies, such as Wohlfahrtia magnifica, Lucilia sericata, Chrysomya megacephala or Musca domestica. These insects are potent vectors for the distribution of W. chitiniclastica causing local or systemic infections originating from wounds infested with fly larvae. However, other potential sources of transmission of W. chitiniclastica have been described such as soil or chicken meat. Infections in humans reported to date comprise wound infections, cellulitis, osteomyelitis and sepsis. This review summarizes all the literature available up to now and gives the current knowledge about this emerging human pathogen. Additionally, four patients with proven W. chitiniclastica infections treated at Dresden University Hospital between 2013 and 2015, are included. Special focus was placed on microbiological identification and antibiotic susceptibility testing of the pathogen. [ABSTRACT FROM AUTHOR]

Relative tuber infestation and quality of two Meloidogyne chitwoodi resistant potato genotypes, AR04-4096 and 2011M1, were compared in glasshouse experiments at initial population density (Pi) = 16 second-stage juveniles (g dry soil)-1 in the presence and absence of the bristle oat, Avena strigosa. When A. strigosa was added, Pfroot+soil (Pf = final population) on both AR04-4096 and 2011M1 increased 130×, Pftuber increased 1.9 and 3.7×, respectively, while Pftuber × fresh root weight (FRW)-1 was the same. Nematode hatch from peel of AR04-4096, without A. strigosa, was delayed by 3 weeks but relative hatching rate was increased. Although the RStuber (RS = Relative Susceptibility) of both AR04-4096 and 2011M1 were lower than 1%, in the presence of A. strigosa tuber quality of 2011M1 dropped below the marketable level, while that of AR04-4096 was hardly affected. We conclude that: i) Pftuber is influenced by root mass; ii) root quality influences nematode hatch; iii) tuber quality is not an estimator for tuber resistance, and the reverse; iv) root resistance is equal to tuber resistance. [ABSTRACT FROM AUTHOR]

Powdery mildew caused by the fungus Blumeria graminis f. sp. hordei (Bgh) is a global disease of barley, and the wild subspecies Hordeum vulgare subsp. spontaneum (Hvs) is the closest relative of cultivated barley (H. vulgare subsp. vulgare). The responses to the pathogen of 363 Hvs accessions maintained by the International Center for Agricultural Research in the Dry Areas (ICARDA) gene bank were assessed. Thirty non-Israeli pathogen isolates representing the global pathogenic diversity were used for testing. Because of genetic heterogeneity within 146 accessions, the results from only 217 accessions are presented and discussed. Additional tests on 152 accessions with homogeneous responses in earlier tests were made by using six Israeli pathogen isolates. There were 154 resistance phenotypes among the set, 141 of which involved single accessions. The six most frequent phenotypes were recorded for 62 accessions, with the most frequent phenotype in 26 accessions that were resistant to all 30 non-Israeli Bgh isolates. The second most frequent phenotype, found in 16 accessions, was susceptible to all 30 non-Israeli isolates. The occurrence of specific resistance was high. The occurrence of specific resistance was high and for breeding barley cultivars the effective resistances can be combined with the resistance gene mlo. In such combinations, the mlo gene prevents rapid increase in the pathogen population from overcoming the given specific resistance, whereas the resistance gene will simultaneously prevent erosion of mlo resistance. A more effective method for achieving durable resistance is accumulation minor resistance genes that are also widely distributed in wild barley. [ABSTRACT FROM AUTHOR]

In order to develop integrated circuit (IC) testing, a new system was suggested using a microprobe array, a four-wire tester, machine vision, and motion control technology. The microprobe array can be automatically aligned with the IC die by an image-processing program in the system. It was found that the operating efficiency of the algorithm was improved by six times by extracting the rectangular edge contour. Several image-processing methods were combined and optimized to calculate the deflection angle, and the linear fitting method was improved. Inaccurate fitting was eliminated by the modified fitting method, and the alignment error was significantly reduced. Although IC electrodes were precisely aligned with the microprobe tips, the compressive displacement of the microprobe also has a greater influence on the electrical testing. The testing resistance was not a stable value until the compressive displacement exceeded 100 \mu \textm . Finally, the effectiveness of the microprobe automatic testing approach was confirmed. The open circuits of the ICs can be detected, and the resistance of the circuits, which are not open circuits, can be automatically measured and evaluated. [ABSTRACT FROM PUBLISHER]

Background: Standardized information about resources availability for HIV-infected patients care in Latin America is scarce. The Latin American Workshop Study Group (TLA-VIH) gathered these data throughout the region. Objectives: The aim of the study was to describe characteristics of centers participating of the TLA-VIH and their availability of resources for HIV care in 2015. Methods: Cross-sectional study with information requested to participant centers in 4 fields: (1) general characteristics of centers, (2) health care staff, (3) resources for HIV care and (4) treatment. We used multiple steps for data validation. Results were analyzed by public or private health care provision and by location of providers in provinces or capital cities. Results: We obtained information from 44 centers on charge of 99,639 patients in 11 countries of Latin America. HIV care is provided by an adequate number of health workers and HIV monitoring by Viral Load with an average of 1.8 measurements per year. Resistance testing at first failure is available for 84% of patients while testing for transmitted drug resistance is only available for 28% of HIV-infected population in this study. One third of patients have been potentially exposed to antiretroviral stock out episodes. Conclusions: We analyze characteristics of HIV care in eleven Spanish speaking countries from Americas and the Caribbean. Public and private centers from provinces and capital cities are included in the sample increasing representativeness of results. In general availability of specialized health care human resources is enough at centers participating in this study, but some limitations in terms of availability of resistance testing and electronic resources is observed as well as episodes of shortage of antiretrovirals. These results support the need to discuss minimal standards for HIV care in Latin America. [ABSTRACT FROM AUTHOR]

The use of Cydia pomonella granulovirus (CpGV) isolates as biological control agents of codling moth (CM) larvae is important in organic and integrated pome fruit production worldwide. The commercially available isolates CpGV-0006, CpGV-R5, and CpGV-V15 have been selected for the control of CpGV resistant CM populations in Europe. In infection experiments, CpGV-0006 and CpGV-R5 were able to break type I resistance and to a lower extent also type III resistance, whereas CpGV-V15 overcame type I and the rarely occurring type II and type III resistance. The genetic background of the three isolates was investigated with next generation sequencing (NGS) tools by comparing their nucleotide compositions to whole genome alignments of five CpGV isolates representing the known genetic diversity of the CpGV genome groups A to E. Based on the distribution of single nucleotide polymorphisms (SNPs) in Illumina sequencing reads, we found that the two isolates CpGV-0006 and CpGV-R5 have highly similar genome group compositions, consisting of about two thirds of the CpGV genome group E and one third of genome group A. In contrast, CpGV-V15 is composed of equal parts of CpGV genome group B and E. According to the identified genetic composition of these isolates, their efficacy towards different resistance types can be explained and predictions on the success of resistance management strategies in resistant CM populations can be made.

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Multidrug-resistant and extensively drug-resistant tuberculosis are recent global health issues, which makes tuberculosis - after the success of short course treatment during the second half of the last century - a major health challenge. Globalisation, health inequalities, competing economic interests and political instability contribute substantially to the spread of drug-resistant strains, which are associated with high rates of morbidity and mortality. Issues such as increasing transmission of drug-resistant strains, poor diagnostic coverage and a lengthy, toxic treatment need to be overcome by innovative approaches to tuberculosis control, prevention, diagnostics and treatment. This review addresses recent developments and future concepts. [ABSTRACT FROM AUTHOR]

In order to investigate the performance of microprobe in integrated circuit (IC) testing, a novel testing system with four-wire cable tester and contact force sensor is deployed using high-density microprobes whose resistance and contact force are automatically measured and saved using LabVIEW. The testing resistance is statistically analyzed for DE1-030EB40-010 type probes with adjusted testing parameters. The results show that the displacement effect is significant for resistance testing. In addition, the testing resistance is not a stable and small value until the displacement exceeds 300 \mum. Furthermore, the velocity of microprobe varying from 25 to 40 mm/s leads to a minimum deviation. The life cycle testing experiments indicate that some microprobe life cycles are >200\,000~times, whereas other life cycles are only 70000 times. It is also found that the contact force is decreased with the increase of life cycles, whereas the decreased contact force results in poor contact between microprobe and IC, which in turn affects the life cycle of the microprobe. [ABSTRACT FROM AUTHOR]

Using a computer simulation of human immunodeficiency virus infection we project that genotype resistance testing at first-line antiretroviral therapy failure is very cost-effective in South Africa. The cost-effectiveness will depend on prevalence of wild-type virus and timely response to genotype results.Background. In resource-limited settings, genotype testing at virologic failure on first-line antiretroviral therapy (ART) may identify patients with wild-type (WT) virus. After adherence counseling, these patients may safely and effectively continue first-line ART, thereby delaying more expensive second-line ART.Methods. We used the Cost-Effectiveness of Preventing AIDS Complications International model of human immunodeficiency virus (HIV) disease to simulate a South African cohort of HIV-infected adults at first-line ART failure. Two strategies were examined: no genotype vs genotype, assuming availability of protease inhibitor–based second-line ART. Model inputs at first-line ART failure were mean age 38 years, mean CD4 173/µL, and WT virus prevalence 20%; genotype cost was $300 per test and delay to results, 3 months. Outcomes included life expectancy, per-person costs (2010 US dollars), and incremental cost-effectiveness ratios (dollars per years of life saved [YLS]).Results. No genotype had a projected life expectancy of 106.1 months, which with genotype increased to 108.3 months. Per-person discounted lifetime costs were $16 360 and $16 540, respectively. Compared to no genotype, genotype was very cost-effective, by international guidance, at $900/YLS. The cost-effectiveness of genotype was sensitive to prevalence of WT virus (very cost-effective when prevalence ≥12%), CD4 at first-line ART failure, and ART efficacy. Genotype-associated delays in care ≥5 months decreased survival and made no genotype the preferred strategy. When the test cost was <$100, genotype became cost-saving.Conclusions. Genotype resistance testing at first-line ART failure is very cost-effective in South Africa. The cost-effectiveness of this strategy will depend on prevalence of WT virus and timely response to genotype results. [ABSTRACT FROM AUTHOR]

Abstract: HIV-1 Protease (PR) and Reverse Transcriptase (RT) genotyping is well established for the management of antiretroviral (ARV) drug therapy, as it is able to detect gene mutations encoding resistance to ARV compounds or drug classes, that are associated with reduced drug susceptibility (i.e. phenotype). A correct phenotypic interpretation from the derived PR–RT genotype (i.e. virtual phenotype), requires a well characterized geno-phenotype correlative database and appropriate statistical predictive models. The applicability of the virtual phenotype for the patient, will, however, not only depend on the accuracy of the statistical models and the database they rely on, but also depend largely on the sequence information that is provided. Since HIV-1 evolves as a complex of closely related but non-identical viral genomes (i.e. quasispecies) it is crucial that the sequencing method used, is able to characterize most of the genetic mixtures that make up the different quasispecies within a single patient. US regulatory agencies require that developers of HIV-1 genotyping assays, determine and report the HIV-1 mixture detection level of their assay. Hence, the mixture scoring sensitivity of the population-based Sanger sequencing method, along with the defined mixture scoring rules, used to drive the virco®TYPE HIV-1 virtual phenotype, was investigated by comparing it to the 454 pyrosequencing technique, which is able to generate the complete viral population sequence. To this end the PR–RT coding sequence of 20 clinical isolates was determined by both sequencing methodologies. The genotyping assay which feeds the virco®TYPE HIV-1 virtual phenotype was able to call automatically 97.5% (i.e. 268 mixtures) and 95.3% (i.e. 326 mixtures) of the mixtures that were present between 25 and 75% and between 20 and 80% in the viral population, as detected by 454. From the not called mixtures, all but one did present a mixture sequence in the Sanger DNA chromatograms, however, with a peak surface area for the second peak that was below the threshold setting for automatic mixture calling in the basecaller software (i.e. 25%). Viral loads ranged from 470 to 629,000copies/mL and exerted no effect on the mixture calling relationship between both sequencing methodologies (R 2 =0.92). In some occasions (i.e. 55 mixtures) the genotyping assay would detect automatically mixtures that were present below 20% in the viral population, when measured by 454. Hence, the mixture scoring sensitivity of the automated high throughput virco®TYPE HIV-1 genotyping assay is currently set at 97.5% and 95.3%, for mixtures present at 25 and 20% in the viral population and may identify occasionally mutations that are present at lower frequencies. These findings were not influenced by the viral load of the examined samples. [Copyright &y& Elsevier]

Objectives: Mechanisms of resistance to ethambutol in Mycobacterium tuberculosis remain inadequately described. Although there is mounting evidence that mutations of codon 306 in embB play a key role, a significant number of phenotypically ethambutol-resistant strains do not carry mutations in this codon. Here, other mutations in the embCAB operon are suggested to be involved in resistance development. [ABSTRACT FROM PUBLISHER]

Antiretroviral therapy has improved continuously. Almost every year a new drug has been approved. Nucleoside analogs still build the backbone of antiretroviral therapy. They inhibit reverse transcriptase and thus the transcription of RNA to DNA. They are combined with non-nucleoside reverse transcriptase inhibitors or protease inhibitors. New therapeutic approaches are attachment or entry inhibitors, integrase inhibitors and maturation inhibitors. Multiple prospective multicenter studies have proven the life prolonging effect of antiretroviral therapy. With the optimal therapy life expectancy of HIV patients is only slightly reduced, similar to that of those with chronic diseases such as diabetes mellitus. One result of the higher age of HIV patients is an increase in concomitant diseases and medications. Drug interactions have to be considered and avoided. There has been a long discussion about the best time point to start antiretroviral therapy. In the late 1990s, every infected patient was treated hoping to eliminate the virus, ignoring the CD4+ cell count and viral load. This caused multiple (long-term) side effects and a rising resistance problem. The guidelines now recommend starting therapy at about 350/μl CD4 lymphocytes. Due to its complexity antiretroviral therapy should be initiated and monitored in specialized centers. [ABSTRACT FROM AUTHOR]

The article reports on the use of the oligonucleotide ligation assay (OLA) as a test for detecting HIV-1 drug resistance mutations in resource-poor areas. The OLA is an inexpensive and sensitive ligase-based point mutation assay used in detecting HIV-1 drug-resistance mutations. HIV-1 specimens were collected from seven international laboratories and used in OLA. It was found that laboratories knowledgeable in molecular techniques can use the OLA.