Hepatitis C subtyping assay failure in UK patients born in sub-Saharan Africa: Implications for global treatment and elimination.

BACKGROUND AND AIMS: The newly developed direct-acting antivirals have revolutionized the treatment of chronic hepatitis C virus (HCV), with cure rates as high as 98% in some cohorts. Although genome sequencing has demonstrated that some subtypes of HCV naturally harbor drug resistance associated substitutions (RAS), these are often overlooked as "rarities." Furthermore, commercial subtyping assays and associated epidemiological findings are skewed towards Western cohorts and whole-genome sequencing can be problematic to deploy without significant infrastructure and training support. We thus aimed to develop a simple, robust and accurate HCV subtyping pipeline, to optimize and streamline molecular detection and sequence-based typing of diverse RAS-containing subtypes. METHODS: HCV serum derived from 146 individuals, whose likely source of infection was from sub-Saharan Africa (SSA) was investigated with a novel panel of single round polymerase chain reaction (PCR) assays targeting NS5B and NS5A genomic regions. Virus subtype assignments were determined by pairwise-distance analysis and compared to both diagnostic laboratory assignments and free-to-use online typing tools. RESULTS: Partial NS5A and NS5B sequences were respectively obtained from 131 to 135 HCV-positive patients born in 19 different countries from SSA but attending clinics in the UK. We determined that routine clinical diagnostic methods incorrectly subtyped 59.0% of samples, with a further 6.8% incorrectly genotyped. Of five commonly used online tools, Geno2Pheno performed most effectively in determining a subtype in agreement with pairwise distance analysis. CONCLUSION: This study provides a simple low-cost pathway to accurately subtype in SSA, guide regional therapeutic choice and assist global surveillance and elimination initiatives.

Evaluation of a sterile, filter-based, in-house method for rapid direct bacterial identification and antimicrobial susceptibility testing using positive blood culture.

This study aimed to assess the performance of our in-house method for rapid direct bacterial identification (ID) and antimicrobial susceptibility testing (AST) using a positive blood culture (BC) broth. For Gram-negative bacteria, 4 mL of BC broth was aspirated and passed through a Sartorius Minisart syringe filter with a pore size of 5 µm. The filtrate was then centrifuged and washed. A small volume of the pellet was used for ID, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and for AST, using automated broth microdilution. For Gram-positive cocci, 4 mL of BC broth was passed through the Minisart syringe filter. Then, 4 mL of sterile distilled water was injected in the direction opposite to that of the filtration to collect the bacterial residue trapped in the filter. Compared with the conventional method performed with pure colonies on agar plates, 94.0% (234/249) were correctly identified using the in-house method, with rates of 91.4% (127/139) and 97.3% (107/110) for Gram-positive and Gram-negative isolates, respectively. Of 234 correctly identified isolates, 230 were assessed by AST. Categorical agreement and essential agreement were 93.3% and 94.5%, respectively, with a minor error rate of 3.8%, a major error rate of 3.4%, and a very major error rate of 1.6%. Our in-house preparation method showed good performance in rapid direct ID and AST using positive BC broths compared to the conventional method. This simple method can shorten the conventional turnaround time for ID and AST by at least 1 day, potentially contributing to better patient management.

The pathway through LC-MS method development: in-house or ready-to-use kit-based methods?

Historically, the determination of low concentration analytes was initially made possible by the development of rapid and easy-to-perform immunoassays (IAs). Unfortunately, typical problems inherent to IA technologies rapidly appeared (e.g. elevated cost, cross-reactivity, lot-to-lot variability, etc.). In turn, liquid chromatography tandem mass spectrometry (LC-MS/MS) methods are sensitive and specific enough for such analyses. Therefore, they would seem to be the most promising candidates to replace IAs. There are two main choices when implementing a new LC-MS/MS method in a clinical laboratory: (1) Developing an in-house method or (2) purchasing ready-to-use kits. In this paper, we discuss some of the respective advantages, disadvantages and mandatory requirements of each choice. Additionally, we also share our experiences when developing an in-house method for cortisol determination and the implementation of an "ready-to-use" (RTU) kit for steroids analysis.

Sepsityper® Kit versus In-House Method in Rapid Identification of Bacteria from Positive Blood Cultures by MALDI-TOF Mass Spectrometry.

In order to further accelerate pathogen identification from positive blood cultures (BC), various sample preparation protocols to identify bacteria with MALDI-TOF MS directly from positive BCs have been developed. We evaluated an in-house method in comparison to the Sepsityper® Kit (Bruker Daltonics, Bremen, Germany) as well as the benefit of an on-plate formic acid extraction step following positive signal by the BACTECTM FX system. Confirmation of identification was achieved using subcultured growing biomass used for MALDI-TOF MS analysis. A total of 113 monomicrobial positive BCs were analyzed. The rates of Gram-positive bacteria correctly identified to the genus level using in-house method and Sepsityper® Kit were 63.3% (38/60) and 81.7% (49/60), respectively (p = 0.025). Identification rates at species level for Gram-positive bacteria with in-house method and Sepsityper® kit were 30.0% (18/60) and 66.7% (40/60), respectively (p < 0.001). Identification rates of Gram-negative bacteria were similar with the in-house method and Sepsityper® Kit. Additional on-plate formic acid extraction demonstrated significant improvement in the identification rate of Gram-positive bacteria at both genus and species level for both in-house (p = 0.001, p < 0.001) and Sepsityper® Kit methods (p = 0.007, p < 0.001). Our in-house method is a candidate for laboratory routines with Sepsityper® Kit as a back-up solution when identification of Gram-positive bacteria is unsuccessful.

New Cell Block Method to Enhance the Cellular Yield in Mucous and/or Bloody Samples.

OBJECTIVE: Cell blocks (CBs) are used to complement cytological diagnosis and for ancillary testing. Dissatisfaction with the cellular yield of the CB is widely recognized. Various techniques have been developed to increase the diagnostic utility of CBs. STUDY DESIGN: We invented a new CB technique to increase cellular yield and diagnostic accuracy suitable especially for mucous and/or bloody cytological samples. RESULTS: The new CB technique is described in detail with illustrations and cases, where it increased the cellular yield and diagnostic accuracy. CBs prepared by this method are suitable also for ancillary techniques, namely immunocytochemistry. CONCLUSIONS: The newly described method showed a better cellular yield in mucous and/or bloody cytological specimens.

Evaluation of an in-house MALDI-TOF MS rapid diagnostic method for direct identification of micro-organisms from blood cultures.

PURPOSE: Bloodstream infections are major causes of morbidity and mortality among hospitalized patients worldwide. Early identification of micro-organisms from blood culture can facilitate earlier optimization of treatment. The objective of this study was to assess an in-house method based on a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platform (Clin-TOF MS) for direct organism identification. METHODOLOGY: We studied the performance of the in-house method for direct identification and the conventional sub-culture method in parallel. Identification from subcultures was analysed with Bruker MS as the reference method. RESULTS: A total of 666 blood cultures with a single micro-organism that flagged positive after no more than a 3-day incubation period were collected. The identification accuracy of the in-house Clin-TOF MS method for direct identification and the sub-culture method was 88.6 and 100 %, respectively. The in-house method exhibited better performance for Gram-negative bacteria than for Gram-positive bacteria (93.3 vs 81.6 %). The accuracy rate for anaerobes was 100 % (3/3). The lowest accurate identification rate was for yeast; this was only 20 %. Lytic Anaerobic/F (LAF) and Plus Aerobic/F (PAF) provided the highest accurate identification rates, and it was noteworthy that the accuracy rate for FAN Aerobic (FA) was 82 %, which is higher than previously reported and showed that the method was effective. CONCLUSION: Our study provides an effective sample preparation method for the direct identification of pathogens from positive blood culture vials via Clin-TOF MS at a very low cost of about $0.5 per sample and with a short turnaround time of about 20 min. This will help clinicians make precise diagnoses and provide targeted prescriptions, reducing the risk of the potential development of resistance.

Multi-element chemical analysis of printed circuit boards - challenges and pitfalls.

Printed circuit boards (PCB) are an essential component of electrical and electronic equipment (EEE) and account for roughly 5% of the mass of EEE. Knowledge about the chemical composition of PCB is crucial to enable an enhanced recycling, especially for elements considered critical regarding their economic importance and supply risk (e.g. precious metals or specialty metals such as tantalum, germanium, gallium). No standard reference methods exist for determining the chemical composition of PCB. Previously published element mass fractions cover a wide range and were produced with numerous methods for sample preparation, digestion, and measurement. This impedes comparability of PCB composition from different studies. To investigate sample- and element-specific effects of applied methods a PCB sample from desktop PC was analysed in two separate labs. One lab applied sample- and element-specific validated methods (aqua regia, HF, H2SO4 blend; ICP-OES, QQQ-ICP-MS), providing reference values, the other applied routine in-house methods (aqua regia; ICP-OES, ICP-MS) to assess the validity of in-house methods for chemical analysis of PCB. A t-test was used to identify elements depicting significant differences between validated and in-house methods. For base metals, in-house methods led to comparable results. For precious, specialty, and hazardous metals as well as REE investigated in this study, significant differences were detected. With respect to all results for in-house methods in this study, the combination of aqua regia and ICP-OES led to less significant differences than aqua regia and ICP-MS. The results show that sample- and element-specific quality assurance is crucial to prevent analytical bias.

Comparison between an in-house method and the ViroSeq™ method for determining mutations for drug resistance in the HIV-1 CRF01_AE subtype circulating in China.

Commercial products for determining the drug-resistance mutations of HIV-1 are expensive and usually focus on a particular HIV-1 subtype. In this study, a more cost-effective in-house method was compared side-by-side with the ViroSeq™ Genotyping System 2.0 for determining resistant mutations in China's most prevalent subtype, CRF01_AE. Plasma samples were obtained from 205 patients infected with HIV-1, and subtypes were verified using the Stanford calibrated population resistance tool. The capacity for determining positive samples was not significantly different between the in-house (93.8%) and ViroSeq™ (96.5%) methods. For the clade of subtype CRF01_AE in particular, complete concordance between the methods was observed for the protease and reverse-transcriptase regions of the HIV-1 pol gene, and concordance for overall DRRMs and HLDRMs was 99.5% and 100%, respectively. Although 51 discordant mutations were found, further analysis verified that most of mutations had minimal impact on antiviral drugs. Excellent overall concordance (97.7%) was achieved for the resistance reports between the two methods for CRF01_AE. Thus, the performance and effectiveness of determining resistance-associated mutations were nearly equivalent between the cost-effective in-house method and the ViroSeq™ system, the greatly potential application of the in-house method in China for many patients infected with HIV-1 located in resource-limited regions.

Validation of a reverse-phase high-performance liquid chromatography method for the determination of amino acids in gelatins by application of 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate reagent.

In-house method validation was conducted to determine amino acid composition in gelatin by a pre-column derivatization procedure with the 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate reagent. The analytical parameters revealed that the validated method was capable of selectively performing a good chromatographic separation for 18 amino acids in less than 40 min; the overall detection and quantitation limit for amino acids fell into ranges of 5.68-12.48 and 36.0-39.0 pmol/µl, respectively; the matrix effect was not observed, and the linearity range was 37.5-1000 pmol/µl. The accuracy (precision and recovery) analyses of the method were conducted under repeatable conditions on different days in random order. Method precision revealed by HorRat values was significantly less than 2, except for histidine with a precision of 2.19, and the method recoveries had a range of 80-115% except for alanine which was recovered at 79.4%. The findings were reproducible and accurately defined, and the method was found to be suited to routine analysis of amino acid composition in gelatin-based ingredients.