The effects of sequencing strategies on Metagenomic pathogen detection using bronchoalveolar lavage fluid samples.

Objectives: Metagenomic next-generation sequencing (mNGS) is a powerful tool for pathogen detection. The accuracy depends on both wet lab and dry lab procedures. The objective of our study was to assess the influence of read length and dataset size on pathogen detection. Methods: In this study, 43 clinical BALF samples, which tested positive via clinical mNGS and were consistent with the diagnosis, were subjected to re-sequencing on the Illumina NovaSeq 6000 platform. The raw re-sequencing data, consisting of 100 million (M) paired-end 150 bp (PE150) reads, were divided into simulated datasets with eight different data sizes (5 M, 10 M, 15 M, 20 M, 30 M, 50 M, 75 M, 100 M) and five different read lengths (single-end 50 bp (SE50), SE75, SE100, PE100, and PE150). Both Kraken2 and IDseq bioinformatics pipelines were employed to analyze the previously diagnosed pathogens in the simulated data. Detection of pathogens was based on read counts ranging from 1 to 10 and RPM values ranging from 0.2 to 2. Results: Our results revealed that increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection. However, a larger data sizes for mNGS require higher economic costs and longer turnaround time for data analysis. Our findings indicate 20 M reads being sufficient for SE75 mode to achieve high recall rates. Additionally, high nucleic acid loads in samples can lead to increased stability in pathogen detection efficiency, reducing the impact of sequencing strategies. The choice of bioinformatics pipelines had a significant impact on recall rates achieved in pathogen detection. Conclusions: Increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection but increase the economic and time costs of sequencing and data analysis. Currently, the 20 M reads in SE75 mode may be the best sequencing option.

Gut microbiota and metabolic biomarkers in metabolic dysfunction-associated steatotic liver disease.

Metabolic dysfunction-associated steatotic liver disease (MASLD), a replacement of the nomenclature employed for NAFLD, is the most prevalent chronic liver disease worldwide. Despite its high global prevalence, NAFLD is often under-recognized due to the absence of reliable noninvasive biomarkers for diagnosis and staging. Growing evidence suggests that the gut microbiome plays a significant role in the occurrence and progression of NAFLD by causing immune dysregulation and metabolic alterations due to gut dysbiosis. The rapid advancement of sequencing tools and metabolomics has enabled the identification of alterations in microbiome signatures and gut microbiota-derived metabolite profiles in numerous clinical studies related to NAFLD. Overall, these studies have shown a decrease in α-diversity and changes in gut microbiota abundance, characterized by increased levels of Escherichia and Prevotella, and decreased levels of Akkermansia muciniphila and Faecalibacterium in patients with NAFLD. Furthermore, bile acids, short-chain fatty acids, trimethylamine N-oxide, and tryptophan metabolites are believed to be closely associated with the onset and progression of NAFLD. In this review, we provide novel insights into the vital role of gut microbiome in the pathogenesis of NAFLD. Specifically, we summarize the major classes of gut microbiota and metabolic biomarkers in NAFLD, thereby highlighting the links between specific bacterial species and certain gut microbiota-derived metabolites in patients with NAFLD.

Immunoinformatics Prediction and Protective Efficacy of Vaccine Candidate PiuA-PlyD4 Against Streptococcus Pneumoniae.

Purpose: This study was designed to evaluate the immune protective efficacy of the novel Streptococcus pneumoniae (S. pneumoniae) protein vaccine PiuA-PlyD4 through immunoinformatics prediction and in vitro and in vivo experiments. Methods: In this study, we conducted immunoinformatics prediction and protection analysis on the fusion protein PiuA-PlyD4. The epitope composition of the vaccine was analyzed based on the prediction of B-cell and helper T-cell epitopes. Meanwhile, the molecular docking of PiuA and TLR2/4 was simulated. After immunizing C57BL/6 mice with the prepared vaccine, the biological safety, immunogenicity and conservation were evaluated. By constructing different infection models and from the aspects of adhesion inhibition and cytokines, the protective effect of the fusion protein vaccine PiuA-PlyD4 on S. pneumoniae infection was explored. Results: PiuA-PlyD4 has abundant B-cell and helper T-cell epitopes and shows a high antigenicity score and structural stability. Molecular docking analysis suggested the potential interaction between PiuA and TLR2/4. The specific antibody titer of fusion protein antiserum was as high as (7.81±2.32) ×105. The protective effect of the immunized mice on nasal and lung colonization was significantly better than that of the control group, and the survival rate against S. pneumoniae infection of serotype 3 reached 50%. Cytokine detection showed that the humoral immune response, Th1, Th2 and Th17 cellular immune pathways were all involved in the process. Conclusion: The study indicates that PiuA-PlyD4, whether the results are predicted by immunoinformatics or experimentally validated in vivo and in vitro, has good immunogenicity and immunoreactivity and can provide effective protection against S. pneumoniae infection. Therefore, it can be considered a promising prophylactic vaccine candidate for S. pneumoniae.

A Case Report of a Novel Isovaleryl-CoA Dehydrogenase Gene Mutation in a Chinese Family with Isovaleric Acidemia.

BACKGROUND: Isovaleric acidemia (IVA) is a rare autosomal-recessive metabolic disorder caused by a genetic deficiency of isovaleryl-CoA dehydrogenase (IVD). Deficiency of IVD leads to the accumulation of organic acids; however, the genotype-phenotype relationship has not been well established. METHODS: Two brothers with acute neonatal IVA in a Chinese family were reported, and their clinical manifestations and examination were described. MS/MS and GCMS were used to perform organic acid analysis of blood samples and urine samples, and the patient's blood was sequenced by NGS and Sanger sequencing of the ivd gene. RESULTS: Sequence analysis of the ivd gene identified compound heterozygous mutations in the patient, the c.250T>C (p.W84R) missense mutation (novel) and the c.466-3_466-2 delCAinsGG splicing mutation, which were inherited from their parents. Various bioinformatics prediction algorithms suggest that the p.W84R missense mutation may destabilize the IVD monomer and reduce its ability to bind to substrates. CONCLUSIONS: Both the clinical and genetic features of this family will help us to further expand the knowledge of IVA.

A candidate reference method and multiple commutable control materials for serum 25-hydroxyvitamin D measurement.

OBJECTIVES: The aim of the current study was to establish a reliable candidate reference method for serum 25-hydroxyvitamin D [25(OH)D] measurement and to assess the commutability of multiple control materials among liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods. METHODS: Serum 25-hydroxyvitamin D2 [25(OH)D2] and 25-hydroxyvitamin D3 [25(OH)D3] together with spiked internal standards were extracted with a one-step approach and then analyzed by LC-MS/MS. The commutability assessment for 25(OH)D was conducted according to the Clinical and Laboratory Standards Institute (CLSI) EP14-A3 protocol. 25(OH)D concentrations in 5 levels of unprocessed serum pools, 7 levels of serum pools spiked with 25(OH)D3 or 25(OH)D2, 3 levels of commercial control materials, 2 levels of spiked bovine serum, and 4 levels of external quality assessment (EQA) materials were measured along with 30 single-donor samples using the candidate reference method and two routine LC-MS/MS methods. RESULTS: The candidate reference method could separate 25(OH)D2 and 25(OH)D3 from 14 potential interfering compounds completely within a 9-min analysis time. Good method precision was obtained, and measurement results on certified reference material NIST SRM 972a were within the uncertainty of the certified values. All candidate materials were assessed commutable for LC-MS/MS methods. CONCLUSIONS: The candidate reference method for serum 25(OH)D measurement is precise, accurate, and robust against interferences and can provide an accuracy base for routine methods. The multiple alternative control materials with commutability among LC-MS/MS methods will facilitate the further standardization for serum 25(OH)D measurement.

The consistency of aminotransferase analysis in China: a comparison of six mainstream aminotransferase routine methods and recalibration using human pooled serum preparations supplemented with human recombinant aminotransferases.

Background: To evaluate the consistency of six mainstream homogeneous systems for aminotransferase measurements and improve the consistency of measurements by applying uniform calibrators.Methods: 200 individual samples were grouped into four sets for assays with and without pyridoxal-5-phosphate (P-5'-P) for Alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Routine assays for the P-5'-P group were compared with a reference measurement procedure (RMP). In the non-P-5'-P group, four routine assays were analyzed in a pairwise method across six method pairs. Recalibration was performed using human serum pools (HSPs) supplemented with human original recombinant aminotransferases (HOR). Data were analyzed by Passing-Bablok regression and Bland-Altman plots.Results: In the P-5'-P group, the mean biases for Ortho and Dimension assays for ALT were 17.0% and -25.4%, respectively; for AST, the mean biases were -9.5% and -9.6%, respectively. In the non-P-5'-P group, the mean deviations ranged from -5.9% to 5.9% for ALT. For AST, the relative deviations ranged from -19.1% to 6.5%. After recalibration, in the P-5'-P group, the relative biases were reduced to -12.2% to 7.7% for ALT and -6.9% to 0.8% for AST. The mean deviations for the non-P-5'-P AST group were reduced remarkably (-3.0% to 3.3%).Conclusion: Assays supplemented with P-5'-P exhibited poor performance against RMP for both ALT and AST. For assays without P-5'-P, AST results showed non-satisfactory comparability for almost all method pairs. Uniform calibrators such as HSPs supplemented with HOR could improve consistency among the mainstream homogeneous systems for the measurement of aminotransferase activity, particularly for AST measurement.

Measurement of serum 17-hydroxyprogesterone using isotope dilution liquid chromatography-tandem mass spectrometry candidate reference method and evaluation of the performance for three routine methods.

OBJECTIVES: Accurate measurements of serum 17-hydroxyprogesterone (17OHP) are essential for diagnosis and treatment monitoring for congenital adrenal hyperplasia patients. The performance of serum 17OHP routine methods remains highly variable that calls for a candidate reference measurement procedure (cRMP) to improve the standardization of serum 17OHP measurements. METHODS: Serum samples spiked with internal standards were extracted with a combination of solid-phase extraction and liquid-liquid extraction. The 17OHP was quantified by the isotope dilution coupled with liquid chromatography/tandem mass spectrometry (ID-LC/MS/MS) with electrospray ionization in positive ion mode. Nine structural analogs of 17OHP were evaluated for interferences. The precision and analytical recovery were assessed. Twenty native and 40 spiked serum for performance evaluation were measured by the cRMP and two clinical LC/MS routine methods. RESULTS: No apparent interferences were found with the 17OHP measurement. The within-run, between-run, and total precision for our method were 0.4-0.8%, 0.6-2.0%, and 1.0-2.1% for four pooled serum (2.46-102.72 nmol/L), respectively. The recoveries of added 17OHP were 100.0-100.2%. For the performance of two LC/MS routine methods, they showed relative deviation ranges of -22.1 to 1.1% and -6.7 to 12.8%, respectively. CONCLUSIONS: We developed and validated a reliable serum 17OHP method using ID-LC/MS/MS. The desirable accuracy and precision of this method enable it to serve as a promising cRMP to improve the standardization for serum 17OHP routine measurements.

Commutability Assessment of Candidate External Quality Assessment Materials for Aminotransferase Activity Measurements Based on Different Approaches in China.

BACKGROUND: Using commutable external quality assessment (EQA) materials is important for monitoring successful harmonization efforts. We assessed the commutability of four human serum pool (HSP) preparations to identify candidate EQA materials for alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activity measurement. METHODS: One set each of 85 clinical samples (CSs) was collected for ALT and AST activity measurement. The 15 candidate EQA materials included four types of HSP preparations (A to D): materials A, C, and D contained human original recombinant (HOR) aminotransferases; materials B was mixed leftover samples. The CSs and 15 candidate EQA materials were analyzed using seven routine assays, and the ln-transformed results were analyzed in 21 assay pairs. Commutability was assessed using Deming regression, with a 95% prediction interval (CLSI approach) and the difference in bias with an error component model (International Federation of Clinical Chemistry and Laboratory Medicine [IFCC] approach). RESULTS: For ALT, all materials were commutable for 14-21 assay pairs according to the CLSI and IFCC approaches. For AST, B01-03 showed commutability for 14-21 assay pairs, and C01-03 and D01-03 showed commutability for no less than 10 assay pairs according to the two approaches. A01-06 were commutable for 9-16 assay pairs according to the CLSI approach, but for 6-9 assay pairs according to the IFCC approach. CONCLUSIONS: Mixed leftover samples showed desirable commutability characteristics as candidate EQA materials for routine aminotransferase activity measurements. Human serum bases supplemented with HOR were commutable for most routine ALT activity measurements.

Development and validation of a candidate reference method for serum cortisol by isotope dilution liquid chromatography-tandem mass spectrometry combined with dextran sulfate-Mg2+ precipitation.

Accurate and precise cortisol measurements are requisite for ensuring appropriate diagnosis and management of diseases related with adrenal or pituitary gland disorders. Prompted by the needs in characterization of certified reference materials and quality assurance for serum cortisol measurements, we developed and evaluated a highly reliable measurement procedure based on isotope dilution liquid chromatography-tandem mass spectrometry (ID LC-MS/MS) combined with dextran sulfate-Mg2+ precipitation as the sample pretreatment. An appropriate amount of serum was accurately weighed and spiked with the isotope labelled internal standard. After precipitation, massive lipids and lipoproteins were removed from serum matrix. The clear supernatant was transferred and extracted with ethyl acetate-hexane solution. The cortisol was analyzed with LC-MS/MS in positive electrospray ionization mode. The within-run and total coefficient of variations (CVs) ranged from 0.3 to 0.6% and 0.7 to 1.2%, respectively, for a concentration range of 76.30 to 768.04 nmol/L. A regression comparison of the results obtained by the present method and the certified values of ERM-DA451 showed agreement with no statistical difference (Y = 1.0092 X-0.7455; 95% CI for the slope, 0.9940 to 1.0212; 95% CI for the intercept, - 3.6575 to 2.6390, r2 = 0.999). All structural analogs of cortisol tested were well resolved from cortisol in 12 min on a phenyl ligand column under an isocratic elution. The limit of quantification was estimated to 5 pg cortisol in absolute amount. This method is accurate and simple and can be served as a candidate reference measurement procedure in establishment of serum cortisol reference system.

Commutability of external quality assessment materials for serum magnesium and calcium measurements.

The commutability of pooled patient sera (PPS) and control materials (CM) should be evaluated to investigate their suitability for use in an external quality assessment (EQA) program. Individual human samples, PPS and CM were analyzed by four routine methods and inductively coupled plasma mass spectrometry reference methods for magnesium and calcium measurements. The commutability was analyzed according to EP14-A3 protocol and the difference in bias approach, respectively. For magnesium measurements, all PPS were commutable and 3/5 CM were commutable for all measurement systems according to the EP14-A3 protocol. For calcium measurements, most PPS were commutable for all measurement systems, but the CM were only commutable with the Cobas c702 system. The IFCC approach produced similar commutability profiles, except that a large number of inconclusive results appeared. The routine methods exhibited excellent linearity and precision. The majority of relative biases between the routine and reference methods were beyond the bias limits. The commutability of the CM and PPS vary depending on which evaluation approach and criterion is applied. Superiority in the commutability of PPS over CM was observed whichever evaluation approach is applied.