Six-sigma and quality planning of TORCH tests in the Peruvian population: a single-center cross-sectional study

Objective To ensure the health of newborns, it is necessary to perform high-quality diagnostic tests. The TORCH panel is a set of tests that identifies infectious pathogens such as Toxoplasma (Toxo) and Cytomegalovirus (CMV) that are common in low-setting populations. We performed TORCH panel quality planning using six sigma in a reference laboratory at Peru. Results This was a cross-sectional study. TORCH tests include Toxo, Rubella, CMV, and Herpes. We processed all samples by fourth-generation ELISA on the GEMINI XCR200 analyzer (Diatron, Budapest, Hungary). We obtained the imprecision from the annual data of the external quality assessment plan and we used the CLSI EP12-A3 guideline. In a total of 44,788 analyses, the average imprecision was 3.69 ± 1.47%, and CMV had lower imprecision (2.3 and 2.6% for IgM and IgG, respectively). Quality planning of the TORCH panel allowed estimating the sigma value that ranged from 4 to 10 (average 7 ± 2 sigma), where rubella had the highest values (10 for IgM and 8 for IgG) while HSV2 had the lowest values (4 for IgM and 5 for IgG). Our results suggest the optimal performance of half of the markers including Toxoplasma, Rubella, and CMV in the Peruvian population.

Genome characteristic of Bordetella parapertussis isolated from Iran

Pertussis also known as whooping cough is a respiratory infection in humans particularly in infants and usually caused by Bordetella pertussis. However, Bordetella parapertussis can also cause a similar clinical syndrome. During 2012 to 2015, from nasal swabs sent from different provinces to the pertussis reference laboratory of Pasture Institute of Iran for pertussis confirmation, seven B. parapertussis isolates were identified by bacterial culture, biochemical tests, and the presence of IS1001 insertion in the genome by real-time PCR. Furthermore, the expression of pertactin (Prn) as one the major virulence factor for bacterial adhesion was investigated using western blot. Moreover, the genomic characteristic of one recently collected isolate, IRBP134, from a seven-month infant was investigated using Illumina NextSeq sequencing protocol. The results revealed the genome with G+C content 65% and genome size 4.7 Mbp. A total of 81 single nucleotide polymorphisms (SNPs) and 13 short insertion and deletions were found in the genome compared to the B. parapertussis 12822 as a reference genome showing ongoing evolutionary changes in our isolate. A phylogeny relationship of IRBP134 was also investigated using global B. parapertussis available genomes.

Retrospective Analysis of Six Years of Acute Flaccid Paralysis Surveillance and Polio Vaccine Coverage Reported by Italy, Serbia, Bosnia and Herzegovina, Montenegro, Bulgaria, Kosovo, Albania, North Macedonia, Malta, and Greece

Here we analyzed six years of acute flaccid paralysis (AFP) surveillance, from 2015 to 2020, of 10 countries linked to the WHO Regional Reference Laboratory, at the Istituto Superiore di Sanità, Italy. The analysis also comprises the polio vaccine coverage available (2015–2019) and enterovirus (EV) identification and typing data. Centralized Information System for Infectious Diseases and Laboratory Data Management System databases were used to obtain data on AFP indicators and laboratory performance and countries’ vaccine coverage from 2015 to 2019. EV isolation, identification, and typing were performed by each country according to WHO protocols. Overall, a general AFP underreporting was observed. Non-Polio Enterovirus (NPEV) typing showed a high heterogeneity: over the years, several genotypes of coxsackievirus and echovirus have been identified. The polio vaccine coverage, for the data available, differs among countries. This evaluation allows for the collection, for the first time, of data from the countries of the Balkan area regarding AFP surveillance and polio vaccine coverage. The need, for some countries, to enhance the surveillance systems and to promote the polio vaccine uptake, in order to maintain the polio-free status, is evident.

Strychnine poisoning due to traditional Chinese medicine: a case series

Background: Strychnine poisoning is rare but possibly fatal. The most reported sources of strychnine poisoning include rodenticides and adulterated street heroin. Here we report a case series of an unusual cause of strychnine poisoning – Strychni semen, a herb known as “maqianzi” in traditional Chinese medicine (TCM). Methods: All cases of strychnine poisoning confirmed by the Hospital Authority Toxicology Reference Laboratory (HATRL, the highest-level clinical toxicology laboratory in Hong Kong) between May 2005 and May 2018 were reviewed. Results: Twelve cases of strychnine poisoning were recorded, and Strychni semen was the exclusive source. Ten (83%) patients presented with muscle spasms, and four (33%) developed typical conscious convulsions. The poisoning was severe in two (17%) patients, moderate in three (25%) and mild in eight (58%). No case fatality was recorded. Three (25%) patients were TCM practitioners and two (17%) were laymen who bought the herb themselves without a proper prescription. Conclusion: The practice of TCM is becoming popular in different parts of the world amid the COVID-19 pandemic. The spectrum of clinical features of strychnine poisoning secondary to Strychni semen are similar to those arising from different origins. Eliciting a history of TCM use, apart from exposure to rodenticides and drugs of abuse, may allow timely diagnosis in patients with compatible clinical features. Enhancement of TCM safety could minimize the hazard.

Evaluation of a phenotypic, point-of-care solution for the detection and quantitative antibiotic susceptibility testing for lower Urinary Tract Infection

Background Urinary tract infections (UTIs) are one of the most common bacterial infections seen in primary care. The current standard for the definitive diagnosis of a UTI is culture and sensitivity testing of a mid-stream urine sample at a clinical laboratory; however, this technique is costly, labour intensive and is not directly relevant clinically - typically taking 2-3 days to yield a result. Study design and Objective This is a nonexperimental cross-sectional study. The aim of this study was to evaluate the efficacy of U-treat, a bioluminescent approach for rapid detection of bacteriuria and quantitative determination of the antimicrobial susceptibility profiles of uropathogens in clinical urine specimens - in under an hour. Method The evaluation was carried out in two UK-based Medical Centres using urine samples from patients presenting with symptoms of a UTI (n=249). The U-treat technology is a two test, two reagent process. Test 1 detects the presence of a bacterial UTI > 104 bacteria/mL (5-10 minutes). Test 2 produces quantitative antibiotic susceptibility (<50 minutes). Only urine samples testing positive for bacteria in Test 1 underwent Test 2 (n=82). U-treat results were compared retrospectively against reference laboratory culture and sensitivity findings. The influence of the technology on patient treatment outcomes was also analysed. Results Relative to reference laboratory analysis, Test 1 showed a sensitivity of 97.1% and specificity of 92.0%. (PPV: 89.3%; NPV: 97.8%). Test 2 produced an overall sensitivity (measurement of true susceptibility) of 94.1% (Predictive value: 96%) and an overall specificity (measurement of true resistance) of 90.5% (Predictive value 86.4%). Analysis of treatment data demonstrated that had the physicians had access to U-treat results at the point of care, the percentage of patients treated successfully would have risen from 68.3% to 92.7%. Conclusion U-treat represents the first technology, world-wide, capable of providing UTI treatment data to physicians at the point of care, in less than 60 minutes.

Prevalence of genotypic antimicrobial resistance in clinical Shiga toxin-producing Escherichia coli in Norway, 2018 to 2020

Introduction. Shiga toxin-producing Escherichia coli (STEC) can cause severe to fatal disease in humans. Antimicrobial treatment is sometimes necessary, but contraindicated due to undesirable clinical outcome. However, recent studies have shown promising outcomes following antimicrobial treatment. Before the establishment of a possible antimicrobial treatment strategy for STEC infections, the prevalence of antimicrobial resistance in STEC needs to be determined. Gap Statement. The resistance status of Norwegian clinical STEC is not known and should be assessed. Aim. We aim to characterize genotypic antimicrobial resistance determinants in clinical STEC in Norway, and determine the prevalence of genotypic resistance in order to inform possible antimicrobial treatment options for STEC infections. Methodology. We included all clinical STEC submitted to the Norwegian Reference Laboratory from March 2018 to April 2020. All samples were whole-genome sequenced and screened for genotypic antimicrobial resistance,virulence determinants and plasmid incompatibility groups. We performed phylogenetic clustering of STEC by core-genome multi-locus sequence typing, and statistical association analyses between isolate characteristics and genotypic resistance. Results. A total of 459 STEC were analysed. For 385 (83.9 %) STEC we did not identify any antimicrobial resistance determinants. Seventy-four STEC (16.1 %) harboured antimicrobial resistance determinants against one or more antimicrobial classes. The most frequent genotypic resistance was identified against aminoglycosides (10.5 %). Thirty-nine STEC (8.5 %) had a multi-drug resistance (MDR) genotype. Genotypic resistance was more prevalent in non-O157 than O157 STEC (P=0.02). A positive association was seen between genotypic resistance and the low-virulent STEC O117:H7 phylogenetic cluster (no. 14) (P<0.001). Genotypic resistance was not significantly associated to high-virulent STEC. STEC O146:H28 and isolates harbouring the plasmid replicon type IncQ1 were positively associated with MDR. Conclusion. The overall prevalence of genotypic resistance in clinical STEC in Norway is low (16.1 %). Genotypic resistance is more prevalent in non-O157 strains compared to O157 strains, and not significantly associated to high-virulent STEC. Resistance to antimicrobials suggested for treatment, especially azithromycin is low and may present an empiric treatment alternative for severe STEC infections.

Large Intra-Age Group Variation in Chromosome Abnormalities in Human Blastocysts

Research Question: Is maternal age only a gross predictor of chromosome abnormalities in human embryos? Design: Here, we evaluated the less-studied variation in chromosome abnormality rates in embryos of patients within the same age group. Patients undergoing IVF and PGD for chromosomal abnormalities in ~127 different IVF clinics were included. PGT-A analysis was performed by a single reference laboratory using array CGH or NGS. To get an estimate of the range of abnormalities observed, the aCGH and NGS data were studied both independently and together. Results: The overall results showed the typical increase in aneuploidy rates with advancing maternal age (AMA) but extensive variability within each age group. Conclusions: Increasing aneuploidy with maternal age has been demonstrated in live births, unborn fetuses, IVF embryos and oocytes. In contrast, post-meiotic and other abnormalities that might lead to mosaicism, polyploidy and haploidy, are commonplace (around 30%), regardless of maternal age. Here we conclude that age is only a gross predictor of chromosome abnormalities in IVF embryos. In contrast to the existing standard of offering PGT-A to AMA patients, the high rate and extreme variation of chromosomal abnormalities in human embryos may warrant PGT-A for further IVF cycles even in younger age groups, especially if a history of increased levels of aneuploidy is evident. Furthermore, better indicators are needed to determine which patients are at a higher risk of producing increased levels of aneuploid embryos.

The estimate of the rubella elimination status in the Russian Federation in 2019

In 2002, the WHO Regional Office for Europe developed a Strategic Program for the Prevention of Measles and Congenital Rubella Infections in the European Region, which was revised in 2004. As a result of the revision, an additional target was set to eliminate endemic rubella in the region by 2010. Rubella is a disease that is well controlled by vaccination, which will determine the theoretical possibility of interrupting its global transmission. Since 2013, the Russian Federation has been implementing the National Rubella Elimination Program. Elimination criteria have been revised as the Program progresses. Currently, the main criterion for rubella elimination is the absence of endemic (local) transmission of the virus for at least 36 months, which should be confirmed by molecular genetic research methods. In addition, in the Russian Federation, an incidence rate of less than 1 case per 1 million population is also used as one of the elimination criteria. The successful implementation of the Program is supported by the fact that since 2013, against the background of a high (over 95%) coverage of preventive vaccinations, there has been a decrease in incidence rates and their stabilization at a level of less than 1 per 1 million population since 2014. Genetic monitoring of rubella virus strains circulating among the population showed the termination of endemic transmission of the virus. During the implementation of the Elimination Program, the prevailing genotypes of the virus circulating in Russia were genotypes 1E and 2B, which have a global distribution. The data obtained from the results of molecular genetic monitoring made it possible to determine that the strains isolated during the period under consideration belong to different clusters, which speaks in favour of their imported character. Considering the above factors: high vaccination coverage, low incidence and lack of endemic transmission of the virus, the WHO Committee on verification of measles and rubella elimination in 2017 awarded the Russian Federation the status of a country that has achieved rubella elimination. The continuation of the phase of elimination of infection is confirmed annually. This article presents the results of a comprehensive assessment of the rubella elimination status in the Russian Federation by specialists from the National Scientific and Methodological Center for Measles and Rubella and WHO EURO Moscow regional reference laboratory for measles and rubella based on epidemiological data and data from molecular genetic studies in 2019.

LUMOS - Low and Intermediate Grade Glioma Umbrella Study of Molecular Guided TherapieS at relapse: Protocol for a pilot study

IntroductionGrades 2 and 3 gliomas (G2/3 gliomas), when combined, are the second largest group of malignant brain tumours in adults. The outcomes for G2/3 gliomas at progression approach the dismal outcomes for glioblastoma (GBM), yet there is a paucity of trials for Australian patients with relapsed G2/3 gliomas compared with patients with GBM. LUMOS will be a pilot umbrella study for patients with relapsed G2/3 gliomas that aims to match patients to targeted therapies based on molecular screening with contemporaneous tumour tissue. Participants in whom no actionable or no druggable mutation is found, or in whom the matching drug is not available, will form a comparator arm and receive standard of care chemotherapy. The objective of the LUMOS trial is to assess the feasibility of this approach in a multicentre study across five sites in Australia, with a view to establishing a national molecular screening platform for patient treatment guided by the mutational analysis of contemporaneous tissue biopsiesMethods and analysisThis study will be a multicentre pilot study enrolling patients with recurrent grade 2/3 gliomas that have previously been treated with radiotherapy and chemotherapy at diagnosis or at first relapse. Contemporaneous tumour tissue at the time of first relapse, defined as tissue obtained within 6 months of relapse and without subsequent intervening therapy, will be obtained from patients. Molecular screening will be performed by targeted next-generation sequencing at the reference laboratory (PathWest, Perth, Australia). RNA and DNA will be extracted from representative formalin-fixed paraffin embedded tissue scrolls or microdissected from sections on glass slides tissue sections following a review of the histology by pathologists. Extracted nucleic acid will be quantified by Qubit Fluorometric Quantitation (Thermo Fisher Scientific). Library preparation and targeted capture will be performed using the TruSight Tumor 170 (TST170) kit and samples sequenced on NextSeq 550 (Illumina) using NextSeq V.2.5 hi output reagents, according to the manufacturer’s instructions. Data analysis will be performed using the Illumina BaseSpace TST170 app v1.02 and a custom tertiary pipeline, implemented within the Clinical Genomics Workspace software platform from PierianDx (also refer to section 3.2). Primary outcomes for the study will be the number of patients enrolled and the number of patients who complete molecular screening. Secondary outcomes will include the proportion of screened patients enrolled; proportion of patients who complete molecular screening; the turn-around time of molecular screening; and the value of a brain tumour specific multi-disciplinary tumour board, called the molecular tumour advisory panel as measured by the proportion of patients in whom the treatment recommendation was refined compared with the recommendations from the automated bioinformatics platform of the reference laboratory testing.Ethics and disseminationThe study was approved by the lead Human Research Ethics Committee of the Sydney Local Health District: Protocol No. X19-0383. The study will be conducted in accordance with the principles of the Declaration of Helsinki 2013, guidelines for Good Clinical Practice and the National Health and Medical Research Council National Statement on Ethical Conduct in Human Research (2007, updated 2018 and as amended periodically). Results will be disseminated using a range of media channels including newsletters, social media, scientific conferences and peer-reviewed publications.Trial registration numberACTRN12620000087954; Pre-results.