Identification and validation of diagnostic biomarkers and immune cell abundance characteristics in bloodstream infection by integrative bioinformatics analysis.

() is an opportunistic pathogen that could cause life-threatening bloodstream infections. The objective of this study was to identify potential diagnostic biomarkers of bloodstream infection. Gene expression dataset GSE33341 was optimized as the discovery dataset, which contained samples from human and mice.

Phenotypic and genetic characterization of daptomycin non-susceptible strains selected by adaptive laboratory evolution.

Background: Daptomycin non-susceptible (DNS) strains pose a serious clinical threat, yet their characteristics remain poorly understood.

Methods: DNS derivatives were generated by exposing strains to subinhibitory concentrations of daptomycin. Competition experiment and growth kinetics experiment were used to observe the growth of bacteria.

The roles of cell wall inhibition responsive protein CwrA in the pathogenicity of .

The ability to form robust biofilms and secrete a diverse array of virulence factors are key pathogenic determinants of , causing a wide range of infectious diseases. Here, we characterized as a VraR-regulated gene encoding a cell wall inhibition-responsive protein (CwrA) using electrophoretic mobility shift assays. We constructed deletion mutants in the genetic background of methicillin-resistant (MRSA) and methicillin-sensitive (MSSA) strains.

Insights into small-molecule compound CY-158-11 antibacterial activity against .

Unlabelled: The widespread prevalence and dissemination of antibiotic-resistant bacteria, coupled with the diminishing supply of new antibiotics, emphasize the pressing necessity for the exploration of innovative antibacterial agents. Previously, we detailed the impact of the small-molecule compound CY-158-11 on biofilm. By hindering adhesion and PIA-mediated biofilm formation, subinhibitory concentrations of CY-158-11 exhibit antibiofilm activity toward .

Phenotypic and genomic analysis of the hypervirulent methicillin-resistant ST630 clone in China.

Methicillin-resistant (MRSA) sequence type 630 (ST630) is a rarely reported lineage worldwide. This study aimed to trace the dissemination of the emerging MRSA ST630 clones in China and investigate their virulence potential. We collected 22 ST630-MRSA isolates from across China and performed whole-genome sequencing analysis and virulence characterization on these isolates.

Biofilm-producing ability of methicillin-resistant Staphylococcus aureus clinically isolated in China.

Background: Staphylococcus aureus, a commensal bacterium, colonizes the skin and mucous membranes of approximately 30% of the human population. Apart from conventional resistance mechanisms, one of the pathogenic features of S. aureus is its ability to survive in a biofilm state on both biotic and abiotic surfaces.

Characteristic of KPC-12, a KPC Variant Conferring Resistance to Ceftazidime-Avibactam in the Carbapenem-Resistant ST11-KL47 Clone Background.

Background: Carbapenem-resistant (CRKP) infections are a great threat to public health worldwide. Ceftazidime-avibactam (CZA) is an effective -lactam/-lactamase inhibitors against CRKP. However, reports of resistance to CZA, mainly caused by carbapenemase (KPC) variants, have increased in recent years.

Characterisation of highly virulent and colistin-resistant ST367-KL1 Klebsiella quasipneumoniae subsp. similipneumoniae Strain.

Objectives: To elucidate the characteristics of a colistin-resistant and hypervirulent Klebsiella quasipneumoniae subsp. similipneumoniae strain (KP8) using whole genome sequencing and various phenotypic assays.

Methods: Antimicrobial susceptibility testing was performed using broth microdilution.

A novel small-molecule compound S-342-3 effectively inhibits the biofilm formation of .

Biofilms are an important virulence factor in and are characterized by a structured microbial community consisting of bacterial cells and a secreted extracellular polymeric matrix. Inhibition of biofilm formation is an effective measure to control infection. Here, we have synthesized a small molecule compound S-342-3, which exhibits potent inhibition of biofilm formation in both MRSA and MSSA.

Metagenomic next-generation sequencing for the identification of infections caused by Gram-negative pathogens and the prediction of antimicrobial resistance.

Objective: The aim of this study was to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) for the identification of Gram-negative bacteria (GNB) infections and the prediction of antimicrobial resistance.

Methods: A retrospective analysis was conducted on 182 patients with diagnosis of GNB infections who underwent mNGS and conventional microbiological tests (CMTs).

Results: The detection rate of mNGS was 96.

Phenotypic and genomic analysis of the hypervirulent ST22 methicillin-resistant in China.

ST22 MRSA (methicillin-resistant ) strains are only sporadically reported in China. Through the phylogenetic reconstruction of 30 ST22 strains from China and 480 ST22 strains from global sources, we found that the global ST22 strains can be divided into three clades (I, II, and III). The China ST22 strains were found primarily in clade II (IIb and IIc) and also in clade III, indicating that the China ST22-MRSA clones have different origins.

Small-Molecule Compound CY-158-11 Inhibits Staphylococcus aureus Biofilm Formation.

Staphylococcus aureus is an important human pathogen and brings about many community-acquired, hospital-acquired, and biofilm-associated infections worldwide. It tends to form biofilms, triggering the release of toxins and initiating resistance mechanisms. As a result of the development of S.

Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital.

Purpose: Metagenomic next-generation sequencing (mNGS) is a powerful yet unbiased method to identify pathogens in suspected infections. However, little is known about its clinical effectiveness. The present study aimed to assess the efficacy of mNGS in routine clinical practice.

Phylogenetic Analysis and Virulence Characteristics of Methicillin-Resistant Staphylococcus aureus ST45 in China: a Hyper-Virulent Clone Associated with Bloodstream Infections.

Methicillin-resistant Staphylococcus aureus (MRSA) sequence type 45 (ST45) was rarely found in China. This study was conducted to trace the transmission and evolution of emerging MRSA ST45 strains in mainland China and explore its virulence. A total of 27 ST45 isolates were included for whole-genome sequencing and genetic characteristic analysis.

Phylogenetic analysis and virulence characteristics of methicillin-resistant ST764-SCC II: an emerging hypervirulent clone ST764-t1084 in China.

Previous studies have shown that the increased prevalent ST764 clone in China, Japan, and other Asian areas. However, the knowledge of the genetic features and virulence characteristics of methicillin-resistant (MRSA) ST764 in China is still limited. In this study, we identified 52 ST764-SCC type II isolates collected from five cities in China between 2014 and 2021.

Small-molecule compound SYG-180-2-2 attenuates virulence by inhibiting hemolysin and staphyloxanthin production.

Multi-drug resistant infection is still a serious threat to global health. Therefore, there is an urgent need to develop new antibacterial agents based on virulence factor therapy to overcome drug resistance. Previously, we synthesized SYG-180-2-2 (CHNOSe), an effective small molecule compound against biofilm.

CGAP-align: a high performance DNA short read alignment tool.

Background: Next generation sequencing platforms have greatly reduced sequencing costs, leading to the production of unprecedented amounts of sequence data. BWA is one of the most popular alignment tools due to its relatively high accuracy. However, mapping reads using BWA is still the most time consuming step in sequence analysis.

Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma.

Background: Glioblastoma arises from complex interactions between a variety of genetic alterations and environmental perturbations. Little attention has been paid to understanding how genetic variations, altered gene expression and microRNA (miRNA) expression are integrated into networks which act together to alter regulation and finally lead to the emergence of complex phenotypes and glioblastoma.

Results: We identified association of somatic mutations in 14 genes with glioblastoma, of which 8 genes are newly identified, and association of loss of heterozygosity (LOH) is identified in 11 genes with glioblastoma, of which 9 genes are newly discovered.

Network quotients: structural skeletons of complex systems.

A defining feature of many large empirical networks is their intrinsic complexity. However, many networks also contain a large degree of structural repetition. An immediate question then arises: can we characterize essential network complexity while excluding structural redundancy? In this article we utilize inherent network symmetry to collapse all redundant information from a network, resulting in a coarse graining which we show to carry the essential structural information of the "parent" network.

Emergence of symmetry in complex networks.

Many real networks have been found to have a rich degree of symmetry, which is a universal structural property of complex networks, yet has been rarely studied so far. One of the fascinating problems related to symmetry is exploration of the origin of symmetry in real networks. For this purpose, we summarized the statistics of local symmetric motifs that contribute to local symmetry of networks.