Whole Genome Sequencing Technologies Research Articles

Whole-genome bisulfite sequencing analysis of circulating tumour DNA for the detection and molecular classification of cancer.

BackgroundCancer cell–specific variation and circulating tumour DNA (ctDNA) methylation are promising biomarkers for non‐invasive cancer detection and molecular classification. Nevertheless, the applications of ctDNA to the early detection and screening of cancer remain highly challenging due to the scarcity of cancer cell–specific ctDNA, the low signal‐to‐noise ratio of DNA variation, and the lack of non‐locus‐specific DNA methylation technologies.MethodsWe enrolled three cohorts of breast cancer (BC) patients from two hospitals in China (BC: n = 123; healthy controls: n = 40). We developed a ctDNA whole‐genome bisulfite sequencing technology employing robust trace ctDNA capture from up to 200 μL plasma, mini‐input (1 ng) library preparation, unbiased genome‐wide coverage and comprehensive computational methods.ResultsA diagnostic signature comprising 15 ctDNA methylation markers exhibited high accuracy in the early (area under the curve [AUC] of 0.967) and advanced (AUC of 0.971) BC stages in multicentre patient cohorts. Furthermore, we revealed a ctDNA methylation signature that discriminates estrogen receptor status (Training set: AUC of 0.984 and Test set: AUC of 0.780). Different cancer types, including hepatocellular carcinoma and lung cancer, could also be well distinguished.ConclusionsOur study provides a toolset to generate unbiased whole‐genome ctDNA methylomes with a minimal amount of plasma to develop highly specific and sensitive biomarkers for the early diagnosis and molecular subtyping of cancer.

Gut microbiome is associated with metabolic syndrome accompanied by elevated gamma-glutamyl transpeptidase in men.

It is predicted that by 2035, metabolic syndrome (MS) will be found in nearly more than half of our adult population, seriously affecting the health of our body. MS is usually accompanied by the occurrence of abnormal liver enzymes, such as elevated gamma-glutamyl transpeptidase (GGT). More and more studies have shown that the gut microbiota is involved in MS; however, the correlation between gut microbiota and MS with elevated GGT has not been studied comprehensively. Especially, there are few reports about its role in the physical examination of the population of men with MS and elevated GGT. By using the whole-genome shotgun sequencing technology, we conducted a genome-wide association study of the gut microbiome in 66 participants diagnosed as having MS accompanied by high levels of GGT (case group) and 66 participants with only MS and normal GGT level (control group). We found that the number of gut microbial species was reduced in participants in the case group compared to that of the control group. The overall microbial composition between the two groups is of significant difference. The gut microbiota in the case group is characterized by increased levels of “harmful bacteria” such as Megamonas hypermegale, Megamonas funiformis, Megamonas unclassified, Klebsiella pneumoniae, and Fusobacterium mortiferum and decreased levels of “beneficial bacteria” such as Faecalibacterium prausnitzii, Eubacterium eligens, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides dorei, and Alistipes putredinis. Moreover, the pathways of POLYAMSYN-PWY, ARG+POLYAMINE-SYN, PWY-6305, and GOLPDLCAT-PWY were also increased in the case group, which may play a role in the elevation of GGT by producing amine, polyamine, putrescine, and endogenous alcohol. Taken together, there are apparent changes in the composition of the gut microbiome in men with MS and abnormal GGT levels, and it is high time to discover specific gut microbiome as a potential therapeutic target in that population. More in-depth studies of relevant mechanism could offer some new methods for the treatment of MS with elevated GGT.

Isolation and characterization of nidovirus and bacterial co-infection from cultured turbot (Scophthalmus maximus) in China

In Liaoning Province, China, mass mortality among turbot (Scophthalmus maximus) was observed in multiple cultured farms in 2021. Aside from hemorrhages in the fins and infrabranchial muscles, no visible damage in the infected fish was observed upon visual inspection. Histopathological examination revealed swollen branchial lamellae ends and severe necrosis in the liver, kidney, and spleen. On the one hand, chinook salmon bafinivirus (CSBV) was isolated and identified in the affected turbot using cell isolation, transmission electron microscopy (TEM) observation, and whole-genome sequencing technology. On the other, based on the 16S rRNA sequence and the analysis of the biochemical characteristics, the dominant strains isolated from the diseased fish were identified as Vibrio scophthalmi, Aeromonas salmonicida, and Vibrio splendidus. Phylogenetic analysis revealed that CSBV strain in this study (CSBV Bces-Sm22) had a high identity homology with CSBV strain Bces-Po19, isolated from Japanese flounder Paralichthys olivaceus in 2019. Furthermore, Vibrio scophthalmi, Vibrio splendidus, and Aeromonas salmonicida were close to China, Spain, and Turkey strains, respectively. In this study, we report the first case of turbot that was naturally co-infected with Chinook salmon bafinivirus (CSBV) and bacteria (Vibrio scophthalmi, Aeromonas salmonicida, and Vibrio splendidus) with high mortality rates.

DNA Methylation Analyses Unveil a Regulatory Landscape in the Formation of Nacre Color in Pearl Oyster Pinctada fucata martensii.

Pearl color is regulated by genetics, biological pigments, and organic matrices and an important factor that influences the pearl economic value. The epigenetic regulation mechanism underlying pearl pigmentation remains poorly understood. In this study, we collected the mantle pallial (MP) and mantle central (MC) of the golden-lipped strain, and MP of the silver-lipped strain of pearl oyster Pinctada fucata martensii. The whole-genome bisulfite sequencing (WGBS) technology was employed to investigate the possible implication of epigenetic factors regulating nacre color variation. Our results revealed approximately 2.5% of the cytosines in the genome of the P. fucata martensii were methylated, with the CG methylation type was in most abundance. Overall, we identified 12, 621 differentially methylated regions (DMRs) corresponding to 3,471 DMR-associated genes (DMGs) between the two comparison groups. These DMGs were principally enriched into KEGG metabolic pathways including ABC transporters, Terpenoid backbone biosynthesis, and fatty acid degradation. In addition, integrating information about DMGs, DEGs, and function annotation indicated eight genes LDLR, NinaB, RDH, CYP, FADS, fn3, PU-1, KRMP as the candidate genes related to pigmentation of nacre color. A further study proved that the pigment in nacre is violaxanthin. The results of our study provide the support that there is an association between nacre color formation and DNA methylation profiles and will help to reveal the epigenetic regulation of nacre pigmentation formation in pearl oyster P. fucata martensii.

Progress in research of genomic epidemiology of pathogenic fungi

Genomic epidemiology, based on whole-genome sequencing technology and bioinformatics analysis, can make up for the shortcomings of traditional molecular typing methods and provide a novel insight for the genetic evolution and transmission of pathogenic fungi. The combination of genetic information and epidemiological methods of pathogenic fungi can predict fungi transmission routes and risks, and provide a theoretical basis for the development of public health strategies for fungi infection prevention and control. This paper summarizes the development of molecular epidemiology and genomic epidemiology, as well as the application of genomic epidemiology methods in the analyses of genetic relationship, origin, evolution, drug resistance, virulence, and genome-wide association of pathogenic fungi, and discusses the development of pathogenic fungi genomic epidemiology.

One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings.

Antimicrobial susceptibility testing (AST) should be fast and accurate, leading to proper interventions and therapeutic success. Clinical microbiology laboratories rely on phenotypic methods, but the continuous improvement and decrease in the cost of whole-genome sequencing (WGS) technologies make them an attractive alternative. Studies evaluating the performance of WGS-based prediction of antimicrobial resistance (AMR) for selected bacterial species have shown promising results. There are, however, significant gaps in the literature evaluating the applicability of WGS as a diagnostics method in real-life clinical settings against the range of bacterial pathogens experienced there. Thus, we compared standard phenotypic AST results with WGS-based predictions of AMR profiles in bacterial isolates without preselection of defined species, to evaluate the applicability of WGS as a diagnostics method in clinical settings. We collected all bacterial isolates processed by all Danish Clinical Microbiology Laboratories in 1 day. We randomly selected 500 isolates without any preselection of species. We performed AST through standard broth microdilution (BMD) for 488 isolates (n = 6,487 phenotypic AST results) and compared results with in silico antibiograms obtained through WGS (Illumina NextSeq) followed by bioinformatics analyses using ResFinder 4.0 (n = 5,229 comparisons). A higher proportion of AMR was observed for Gram-negative bacteria (10.9%) than for Gram-positive bacteria (6.1%). Comparison of BMD with WGS data yielded a concordance of 91.7%, with discordant results mainly due to phenotypically susceptible isolates harboring genetic AMR determinants. These cases correspond to 6.2% of all isolate-antimicrobial combinations analyzed and to 6.8% of all phenotypically susceptible combinations. We detected fewer cases of phenotypically resistant isolates without any known genetic resistance mechanism, particularly 2.1% of all combinations analyzed, which corresponded to 26.4% of all detected phenotypic resistances. Most discordances were observed for specific combinations of species-antimicrobial: macrolides and tetracycline in streptococci, ciprofloxacin and β-lactams in combination with β-lactamase inhibitors in Enterobacterales, and most antimicrobials in Pseudomonas aeruginosa. WGS has the potential to be used for surveillance and routine clinical microbiology. However, in clinical microbiology settings and especially for certain species and antimicrobial agent combinations, further developments in AMR gene databases are needed to ensure higher concordance between in silico predictions and expected phenotypic AMR profiles.

Integrating Genetic Structural Variations and Whole-Genome Sequencing Into Clinical Neurology.

Advances in genome sequencing technologies have unlocked new possibilities in identifying disease-associated and causative genetic markers, which may in turn enhance disease diagnosis and improve prognostication and management strategies. With the capability of examining genetic variations ranging from single-nucleotide mutations to large structural variants, whole-genome sequencing (WGS) is an increasingly adopted approach to dissect the complex genetic architecture of neurologic diseases. There is emerging evidence for different structural variants and their roles in major neurologic and neurodevelopmental diseases. This review first describes different structural variants and their implicated roles in major neurologic and neurodevelopmental diseases, and then discusses the clinical relevance of WGS applications in neurology. Notably, WGS-based detection of structural variants has shown promising potential in enhancing diagnostic power of genetic tests in clinical settings. Ongoing WGS-based research in structural variations and quantifying mutational constraints can also yield clinical benefits by improving variant interpretation and disease diagnosis, while supporting biomarker discovery and therapeutic development. As a result, wider integration of WGS technologies into health care will likely increase diagnostic yields in difficult-to-diagnose conditions and define potential therapeutic targets or intervention points for genome-editing strategies.

Whole-Genome Sequence Resource of Fusarium oxysporum Strain TH15, a Plant Growth Promoting Endophytic Fungus Isolated from Tetrastigma hemsleyanum

Whole-Genome Sequence Resource of <i>Fusarium oxysporum</i> Strain TH15, a Plant Growth Promoting Endophytic Fungus Isolated from <i>Tetrastigma hemsleyanum</i>

Whole-genome sequence analysis through online web interfaces: a review.

The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.

Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field.

The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.

Monitoring and managing SARS-CoV-2 evolution in immunocompromised populations

Monitoring and managing SARS-CoV-2 evolution in immunocompromised populations

Whole-genome sequencing identifies rare missense variants of WNT16 and ERVW-1 causing the systemic lupus erythematosus

Systemic lupus erythematosus (SLE, OMIM 152700) is a rare autoimmune disease with high heritability that affects ~0.1% of the population. Previous studies have revealed several common variants with small effects in European and East Asian SLE patients. However, there is still no rare variant study on Chinese SLE patients using the whole-genome sequencing technology (WGS). Here, we designed a family based WGS study to identify novel rare variants with large effects. Based on large-scale allele frequency data from the gnomAD database, we identified rare protein-coding gene variants with disruptive and sequence-altering impacts in SLE patients. We found that the burden of rare variants was significantly higher than that of common variants in patients, suggesting a larger effect of rare variants on the SLE pathogenesis. We identified the pathogenic risk of rare missense variants with significant odds ratios (p < 0.05) in two genes, including WNT16 (NC_000007.14:g.121329757G > C, NP_057171.2:p.(Ala86Pro) and 7 g.121329760G > C, NP_057171.2:p.(Ala87Pro)), which explains five out of seven patients covering all three families but are absent from all controls, and ERVW-1 (NC_000007.14:g.92469882A > G, NP_001124397.1:p.(Leu167Pro), rs74545114; NC_000007.14:g.92469907G > A, NP_001124397.1:p.(Arg159Cys), rs201142302; NC_000007.14:g.92469919G > A, NP_001124397.1:p.(His155Tyr), rs199552228), which explains the other two patients. None of these variants were identified in any of the controls. These associations are supported by known gene expression studies in SLE patients based on literature review. We further tested the wild and mutant types using the luciferase assays and qPCR in cells. We found that WNT16 can activate the canonical Wnt/β-catenin pathway while the mutant cannot. Additionally, the wild ERVW-1 expression can be significantly up-regulated by cAMP while the mutant cannot. Our study provides the first direct genetic and in vitro evidence for the pathogenic risk of mutant WNT16 and ERVW-1, which may facilitate the design of precision therapy for SLE.

One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods.

ObjectivesImplementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark.MethodsWe performed a point-prevalence study of all bacterial isolates (n = 2,009) processed and reported in the Clinical Microbiology Laboratories in Denmark in one day in January 2018. We compared species identification as performed by classical methods (MALDI-TOF) and by bioinformatics analysis (KmerFinder and rMLST) of WGS (Illumina NextSeq) data. We compared the national point-prevalence of bacterial isolates observed in clinical settings with the research attention given to those same genera in scientific literature.ResultsThe most prevalent bacterium was Escherichia coli isolated from urine (n = 646), followed by Staphylococcus spp. from skin or soft tissues (n = 197). The distribution of bacterial species throughout the country was not homogeneous. We observed concordance of species identification for all methods in 95.7% (n = 1,919) of isolates, furthermore obtaining concordance for 99.7% (n = 1,999) at genus level. The number of scientific publications in the country did not correlate with the number of bacterial isolates of each genera analysed in this study.ConclusionsWGS technologies have the potential to be applied in clinical settings for routine diagnostics purposes. This study also showed that bioinformatics databases should be continuously improved and results from local point-prevalence surveys should not be applied at national levels without previously determining possible regional variations.

Microbial Characteristics and Genomic Analysis of an ST11 Carbapenem-Resistant Klebsiella pneumoniae Strain Carrying bla KPC-2 Conjugative Drug-Resistant Plasmid.

BackgroundThe sequence type 11 (ST11) carbapenem-resistant Klebsiella pneumoniae (CRKP) carrying blaKPC−2 has been widespread all over the world, and it has been reported frequently in China. The blaKPC−2 located on the mobile genetic element brings tremendous pressure to control the spread and outbreak of resistant bacteria. Whole-genome sequencing (WGS) technology can comprehensively and in-depth display the molecular characteristics of drug-resistant bacteria, providing a basis for evaluating the genetic diversity within the CRKP genome.MethodsThe ST11 CRKP in this study was collected in the intensive care unit of a major teaching hospital. PCR and Sanger sequencing confirmed the existence of blaKPC−2. The AST-GN card and the microbroth dilution test were used for antimicrobial susceptibility testing. The transferability of plasmid was verified by a conjugation test. The whole genome is sequenced using the Illumina HiSeq short-read and Oxford Nanopore long-read sequencing technology.ResultsThe studied strain was named CRKP63, which is a multi-drug resistance bacteria, which carries blaKPC−2 and blaSHV−182. Its genome consists of a circular chromosome of 5,374,207 bp and an IncFII plasmid named pKPC-063001 of 359,625 bp. In the drug-resistant plasmid pKPC-063001, the key carbapenem resistance gene blaKPC−2 was located in the genetic context with insertion sequence ISKpn27 upstream and ISKpn6 downstream and bracketed by IS26. The three copies of the IS26–ISKpn27–blaKPC−2–ISKpn6–IS26 unit were present in tandem. blaKPC−2 can be transferred horizontally between other species by conjugation, the complete type IV secretion system (T4SS) structure helps to improve the adaptability of bacteria to the external environment, strengthen the existence of drug-resistant bacteria, and accelerate the spread of drug resistance.ConclusionHigh-throughput sequencing has discovered the different surrounding environments of blaKPC−2, which provides a new idea for further revealing the transmission and inheritance of blaKPC−2 at the molecular level. In order to control the further spread and prevalence of drug-resistant bacteria, we should pay close attention to the changes in the genetic environment of blaKPC−2 and further study the transcription and expression of T4SS.

Predicting Physical Appearance from DNA Data-Towards Genomic Solutions.

The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.

Comparative methylomics and chromatin accessibility analysis in Osmanthus fragrans uncovers regulation of genic transcription and mechanisms of key floral scent production.

Linalool and ionone are two important aromatic components in sweet osmanthus petals, and the regulatory mechanisms that produce these two components remain unclear. In this study, we employed whole-genome methylation sequencing and ATAC-seq technology to analyze the genomic DNA methylation status and chromatin accessibility of the sweet osmanthus cultivars ‘Zaohuang’ and ‘Chenghong Dangui’. Results showed that the promoter region of TPS2, a key gene in the linalool synthesis pathway, was less methylated in ‘Chenghong Dangui’ than in ‘Zaohuang’. The chromatin was more accessible in ‘Chenghong Dangui’ than in ‘Zaohuang’, which resulted in a much stronger expression of this gene in ‘Chenghong Dangui’ than in ‘Zaohuang’. This eventually led to a high quantity of linalool and its oxides in the petals of ‘Chenghong Dangui’, but there were lower levels present in the petals of ‘Zaohuang’. These results suggest that DNA methylation and chromatin accessibility play major roles in linalool synthesis in sweet osmanthus. The methylation level of the promoter region of CCD4, a key gene for ionone synthesis, was higher in ‘Zaohuang’ than in ‘Chenghong Dangui’. The chromatin accessibility was lower in ‘Zaohuang’ than in ‘Chenghong Dangui’, although the expression of this gene was significantly higher in ‘Zaohuang’ than in ‘Chenghong Dangui’. ChIP-seq analysis and a series of experiments showed that the differential expression of CCD4 and CCD1 in the two cultivars may predominantly be the result of regulation by ERF2 and other transcription factors. However, a 183-bp deletion involving the CCD4 promoter region in ‘Chenghong Dangui’ may be the main reason for the low expression of this gene in its petals. This study provides an important theoretical basis for improving selective breeding of key floral fragrance components in sweet osmanthus.

Genomic surveillance: a potential shortcut for effective Chagas disease management.

Chagas disease is an enduring public health issue in many Latin American countries, receiving insufficient investment in research and development. Strategies for disease control and management currently lack efficient pharmaceuticals, commercial diagnostic kits with improved sensitivity, and vaccines. Genetic heterogeneity of Trypanosoma cruzi is a key aspect for novel drug design since pharmacological technologies rely on the degree of conservation of parasite target proteins. Therefore, there is a need to expand the knowledge regarding parasite genetics which, if fulfilled, could leverage Chagas disease research and development, and improve disease control strategies. The growing capacity of whole-genome sequencing technology and its adoption as disease surveillance routine may be key for solving this long-lasting problem.

Whole-Genome Sequence Datasets: A Powerful Resource for the Food Microbiology Laboratory Toolbox

Whole-genome sequencing (WGS) technologies are rapidly being adopted for routine use in food microbiology laboratories worldwide. Examples of how WGS is used to support food safety testing include gene marker discovery (e.g., virulence and anti-microbial resistance gene determination) and high-resolution typing (e.g., cg/wgMLST analysis). This has led to the establishment of large WGS databases representing the genomes of thousands of different types of food pathogenic and commensal bacteria. This information constitutes an invaluable resource that can be leveraged to develop and validate routine test methods used to support regulatory and industry food safety objectives. For example, well-curated raw and assembled genomic datasets of the key food pathogens (Salmonella enterica, Listeria monocytogenes, and Shiga-toxigenic Escherichia coli) have been used in our laboratory in studies to validate bioinformatics pipelines, as well as new molecular methods as a prelude to the laboratory phase of the “wet lab” validation process. The application of genomic information to food microbiology method development will decrease the cost of test development and lead to the generation of more robust methodologies supporting risk assessment and risk management actions.

A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC bla NDM-1- and armA-carrying Plasmid.

Background.Patients colonized with multiple species of carbapenemase-producing Enterobacterales (CPE) are increasingly observed. This phenomenon can be due to the high local prevalence of these pathogens, the presence of important host risk factors, and the great genetic promiscuity of some carbapenemase genes.Methods.We analyzed 4 CPE (Escherichia coli, Klebsiella pneumoniae, Providencia stuartii, Citrobacter sedlakii), 1 extended-spectrum cephalosporin-resistant K. pneumoniae (ESC-R-Kp), and 1 carbapenemase-producing Acinetobacter baumannii simultaneously isolated from a patient transferred from Macedonia. Susceptibility tests were performed using a microdilution MIC system. The complete genome sequences were obtained by using both short-read and long-read whole-genome sequencing technologies.Results.All CPE presented high-level resistance to all aminoglycosides due to the expression of the armA 16S rRNA methylase. In C. sedlakii and E. coli (ST69), both the carbapenemase blaNDM-1 and armA genes were located on an identical IncC plasmid of type 1a. The K. pneumoniae (ST268) and P. stuartii carried chromosomal blaNDM-1 and blaOXA-48, respectively, while the ESC-R-Kp (ST395) harbored a plasmid-located blaCTX-M-15. In the latter 3 isolates, armA-harboring IncC plasmids similar to plasmids found in C. sedlakii and E. coli were also detected. The A. baumannii strain possessed the blaOXA-40 carbapenemase gene.Conclusions.The characterization of the genetic organization of IncC-type plasmids harbored by 3 different species from the same patient offered insights into the evolution of these broad-host-range plasmids. Moreover, we characterized here the first complete genome sequence of a carbapenemase-producing C. sedlakii strain, providing a reference for future studies on this rarely reported species.

Structural and Functional Alterations of Gut Microbiota in Males With Hyperuricemia and High Levels of Liver Enzymes.

Objective: To investigate the correlation between the structure and function alterations of gut microbiota and biochemical indicators in males with hyperuricemia (HUA) and high levels of liver enzymes, in order to provide new evidences and therapeutic targets for the clinical diagnosis and treatment of HUA.Methods: A total of 69 patients with HUA (HUA group) and 118 healthy controls were enrolled in this study. Their age, height, waist circumference, weight, and pressure were measured. The clinical parameters such as fasting plasma glucose (FBG), aspartate aminotransferase (AST), alanine aminotransferase (ALT), serum uric acid (SUA), serum creatinine (Scr), total cholesterol (TC), triglyceride (TG), low-density lipoprotein (LDL), high-density lipoprotein (HDL), white blood cell (WBC), platelet (PLT), and absolute value of neutrophils (NEUT) were examined. We used whole-genome shotgun sequencing technology and HUMAnN2 MetaCyc pathway database to detect the composition and pathways of the gut microbiota. The main statistical methods were student's t test, chi-square tests, and Wilcoxon rank sum test. The correlations among bacterial diversity, microbial pathways, and biochemical indicators were evaluated by the R function “cor.test” with spearman method.Results: The gut bacterial diversity in HUA group reduced significantly and the community of the microbiota was of significant difference between the two groups. The pathways that can produce 5-aminoimidazole ribonucleotide (PWY-6122, PWY-6277, and PWY-6121), aromatic amino acids, and chorismate (COMPLETE-ARO-PWY, ARO-PWY, and PWY-6163) were enriched in the HUA group; while the pathways that can produce short-chain fatty acids (SCFAs, such as CENTFERM-PWY and PWY-6590) and the gut microbiotas that can produce SCFAs (Roseburia hominis, Odoribacter splanchnicus, Ruminococcus callidus, Lachnospiraceae bacterium 3_1_46FAA, Bacteroides uniformis, Butyricimonas synergistica) and equol (Adlercreutzia equolifaciens) were enriched in healthy controls.Conclusion: The structure and function of the gut microbiota in males with HUA and high levels of liver enzymes have altered apparently. In-depth study of related mechanisms may provide new ideas for the treatment of HUA.