Implementable assay for monitoring minimum residual disease after radical treatment for colorectal cancer.

Considering the cost and invasiveness of monitoring postoperative minimal residual disease (MRD) of colorectal cancer (CRC) after adjuvant chemoradiotherapy (ACT), we developed a favorable approach based on methylated circulating tumor DNA to detect MRD after radical resection. Analyzing the public database, we identified the methylated promoter regions of the genes FGD5, GPC6, and MSC. Using digital polymerase chain reaction (dPCR), we termed the "amplicon of methylated sites using a specific enzyme" assay as "AMUSE.

CRISPR gel: A one-pot biosensing platform for rapid and sensitive detection of HIV viral RNA.

CRISPR technology has recently emerged as a powerful biosensing tool for sensitive and specific nucleic acid detection when coupled with isothermal amplification (e.g., recombinase polymerase amplification (RPA)).

Bioinspired CRISPR-Mediated Cascade Reaction Biosensor for Molecular Detection of HIV Using a Glucose Meter.

HIV molecular detection plays a significant role in early diagnosis and antiretroviral therapy for HIV patients. CRISPR technology has recently emerged as a powerful tool for highly sensitive and specific nucleic acid based molecular detection when used in combination with isothermal amplification. However, it remains a challenge to improve the compatibility of such a multienzyme reaction system for simple and sensitive molecular detection.

Single-tube one-step gel-based RT-RPA/PCR for highly sensitive molecular detection of HIV.

We developed a single-tube one-step gel-based reverse transcription-recombinase polymerase amplification (RT-RPA)/polymerase chain reaction (PCR) (termed "SOG RT-RPA/PCR") to detect the human immunodeficiency virus (HIV). To improve the assay sensitivity, the RNA template is pre-amplified by RT-RPA prior to PCR. To simplify the detection process and shorten the assay time, we embedded PCR reagents into agarose gel, constructing it to physically separate the reagents from the RT-RPA reaction solution in a single tube.

Rapid detection and surveillance of cfiA-positive Bacteroides fragilis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Objectives: To perform surveillance of cfiA-positive Bacteroides fragilis using new subtyping software module, MALDI Biotyper Subtyping Module (MBT Subtyping Module), on MALDI-TOF MS system, and to evaluate the detection ability of the module.

Methods: cfiA-positive strains were presumed using the module against B. fragilis isolated between 2006 and 2019.

Had COVID-19 spread in the community before the first confirmed case in Nagasaki, Japan?

This retrospective study evaluated stored nasopharyngeal swab samples from Japanese patients with influenza-like illness during the 2019/2020 season. We aimed to determine whether COVID-19 had spread in the community before the first confirmed case. The period of influenza season during 2019/2020 in Nagasaki was shorter than in previous influenza seasons.

A Methodology for Assessing Tumor Clonality of Adult T Cell Leukemia/Lymphoma.

While clonal heterogeneity has been demonstrated in most cancers, quantitative assessment of individual tumor clones has not been translated to inform clinical practice. A few methods have been developed to investigate the tumor clonality of adult T cell leukemia/lymphoma (ATLL), but currently there is no clinically translatable method available for quantifying individual tumor clones in ATLL patients. Here, we present a methodology to assess the tumor clonality of ATLL and quantify patient-specific tumor clones in a clinical setting.

A novel macrolide, solithromycin suppresses mucin overexpression induced by Pseudomonas aeruginosa LPS in airway epithelial cells.

Some macrolides such as 14- and 15-membered macrolides have immunomodulatory effects such as suppression of mucin overproduction. Because a novel macrolide, solithromycin, was developed, we examined whether it suppresses the overexpression of mucin in vitro. A human airway epithelial cell line NCI-H292 was stimulated by Pseudomonas aeruginosa lipopolysaccharides to induce the overproduction of a major mucin, MUC5AC.

Flow cytometry assay for the detection of single-copy DNA in human lymphocytes.

Specific nucleic acid sequences can be detected in individual cells by in situ hybridization. However, when very few copies of a target sequence are present per cell, its signal is undetectable by flow cytometry. Although various approaches have been developed to increase fluorescence signals for in situ hybridization, flow cytometric detection of specific genomic DNA sequences has not been established.

Effect of probiotics on gut microbiome in patients with administration of surgical antibiotic prophylaxis: A randomized controlled study.

Surgical antibiotic prophylaxis (SAP) is recommended for the prevention of surgical site infections. However, there is a concern about adverse effects of SAP, such as antibiotic-associated diarrhea (AAD). To prevent AAD, administration of probiotics has been investigated.

The Effect of In Vitro Hemolysis on Measurement of Cell-Free DNA.

Background: Hemolysis during blood drawing is a common cause of laboratory artifacts. Although circulating cell-free tumor DNA and fetal DNA are currently measured in routine practice, the effect of in vitro hemolysis on the measurement of cell-free DNA (cfDNA) has not been investigated. When in vitro hemolysis occurs, cellular DNA could be released from damaged white blood cells and reduce the fraction of circulating tumor DNA and fetal DNA.

Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model.

The alteration of the microbial community in the upper respiratory tract (URT) can contribute to the colonization and invasion of respiratory pathogens. However, there are no studies regarding whether the characteristics of the URT microbiota can be affected by infections in lower respiratory tract (LRT). To elucidate the microbial profiles of the URT during pneumonia, the oral, nasal, and lung microbiota was evaluated at the early phase in a murine pneumonia model by direct intratracheal inoculation of Klebsiella pneumoniae.

Detection of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae using the MALDI Biotyper Selective Testing of Antibiotic Resistance-β-Lactamase (MBT STAR-BL) assay.

The MALDI Biotyper Selective Testing of Antibiotic Resistance-β-Lactamase (MBT STAR-BL) assay, which analyzes bacterial induced hydrolysis of cefotaxime using MALDI-TOF MS, correctly identified 100.0% of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae as positive and 94.7% of non-ESBL producers as negative in 80 strains tested.

Molecular epidemiology of Clostridioides difficile and risk factors for the detection of toxin gene-positive strains.

In this study, we investigated all Clostridioides difficile strains isolated from stool samples in Nagasaki University Hospital between January 2012 and December 2014. Toxin genes (tcdA, tcdB and cdtA/cdtB) were analyzed for multiplex PCR in a total of 213 strains. In the toxin gene-positive strain, PCR ribotyping was conducted using capillary gel electrophoresis-based PCR and the Webribo database.

Performance evaluation of the MALDI Biotyper Selective Testing of Antibiotic Resistance-β-Lactamase (MBT STAR-BL) assay for the detection of IMP metallo-β-lactamase activity in Enterobacteriaceae.

The MALDI Biotyper Selective Testing of Antibiotic Resistance-β-Lactamase (MBT STAR-BL) assay enables rapid detection of β-lactamase activity using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. The assay is based on analysis of bacterially induced hydrolysis of β-lactam antibiotics. We investigated the performance of the MBT STAR-BL assay for detecting IMP metallo-β-lactamase (MBL) activity in Enterobacteriaceae.

Evaluation of FilmArray respiratory panel multiplex polymerase chain reaction assay for detection of pathogens in adult outpatients with acute respiratory tract infection.

Although viruses are the major pathogen that causes upper respiratory tract infection (URTI) and acute bronchitis, antibiotics have been prescribed. This was a prospective observational study in influenza epidemics that enrolled adult outpatients who visited a hospital with respiratory tract infection symptoms. In this study, we evaluated the usefulness of FilmArray respiratory panel (RP).

Activity of Lascufloxacin against Streptococcus pneumoniae with Mutations in the Quinolone Resistance-Determining Regions.

Lascufloxacin showed potent activity against with a GyrA or ParC mutation (first-step mutant). The frequency of selecting resistant strains tended to be lower for lascufloxacin than for levofloxacin and garenoxacin after drug exposure in first-step mutants but was similar in the comparison between lascufloxacin and moxifloxacin. The increase in MIC was smaller for lascufloxacin than for levofloxacin, garenoxacin, and moxifloxacin when clinical strains with only ParC mutations were exposed to the corresponding drug.

Strong influence of human leukocyte antigen-DP variants on response to hepatitis B vaccine in a Japanese population.

Genome-wide association studies (GWASs) have reported that human leukocyte antigen (HLA) variants are associated with chronic hepatitis B, spontaneous hepatitis B virus (HBV) clearance, and response to hepatitis B vaccine. Single nucleotide polymorphisms (SNPs) in HLA-DP (rs9277535 and rs3077) and HLA-DQ (rs2856718 and rs7453920) have been repeatedly associated with chronic hepatitis B and spontaneous HBV clearance. However, the data on the SNPs associated with response to hepatitis B vaccine are inconclusive.