Novel allelic variations in Tannin1 and Tannin2 contribute to tannin absence in sorghum.

Sorghum is an important food crop commonly used for brewing, feed, and bioenergy. Certain genotypes of sorghum contain high concentrations of condensed tannins in seeds, which are beneficial, such as protecting grains from herbivore bird pests, but also impair grain quality and digestibility. Previously, we identified Tannin1 and Tannin2, each with three recessive causal alleles, regulate tannin absence in sorghum. In this study, via characterizing 421 sorghum accessions, we further identified three novel recessive alleles from these two genes. The tan1-d allele contains a 12-bp deletion at position 659 nt and the tan1-e allele contains a 10-bp deletion at position 771 nt in Tannin1. The tan2-d allele contains a C-to-T transition, which results in a premature stop codon before the bHLH domain in Tannin2, and was predominantly selected in China. We further developed KASP assays targeting these identified recessive alleles to efficiently genotype large populations. These studies provide new insights in sorghum domestication and convenient tools for breeding programs. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01463-y.

Laparoscopic continent cutaneous urinary diversion using a modified Yang-Monti technique in an adult: A case report including 5-year follow-up.

Continuous cutaneous urinary diversion is challenging when the appendix is physically unavailable. The Yang-Monti channel is an alternative to the tunneled appendix for urinary diversion. We present a case involving a 49-year-old man who underwent total urethrectomy and cystostomy 10 months previously. No tumor recurrence was observed; however, the patient experienced severe catheter-related bladder irritation after the procedure. The patient was readmitted to the authors' hospital and underwent laparoscopic continent cutaneous urinary diversion using extracorporeal construction of a modified Yang-Monti channel. The operation lasted 232 minutes, with an estimated blood loss of 10 mL. The patient was discharged from hospital 6 days after surgery and removal of the cystostomy tube. After this, clean intermittent catheterization was performed every 3 hours for 4 weeks. Five years after the procedure, the modified Yang-Monti channel was still used for clean intermittent catheterization without any stomal stenosis being observed. The patient was satisfied with his postoperative quality of life.

Monitoring the long-term spatiotemporal transmission dynamics and ecological surveillance of multidrug-resistant Salmonella enterica serovar Goldcoast: A multicenter genomic epidemiology study.

The emergence of multidrug-resistant Salmonella enterica serovar Goldcoast poses a significant threat to the effective treatment and control of salmonellosis within the ecological environment. Here, we conducted a genomic epidemiological study delineate the global dissemination scenarios of the multidrug-resistant S. Goldcoast originated from 11 countries for over 20 years. The population structure and evolutionary history of multidrug-resistant S. Goldcoast was investigated through phylogenomic and long-term spatiotemporal transmission dynamic analysis. ST358 and ST2529 are the predominant lineages of S. Goldcoast. Multidrug-resistant S. Goldcoast strains have mainly been identified in the ST358 lineage from human and the ST2529 lineage from livestock. ST358 S. Goldcoast was estimated to have emerged in the United Kingdom in 1969, and then spread to China, with both countries serve as centers for the global dissemination of the ST358 lineage. After its emergence and subsequent spread in Chinese clinical and environmental samples, occasional instances of this lineage have been reported in Canada, the United Kingdom, and Ireland. Clonal transmission of ST358 and ST2529 S. Goldcoast have occurred not only on an international and intercontinental scale but also among clinical, environmental and livestock samples. These data indicated that international circulation and local transmission of S. Goldcoast have occurred for over a decade. Continued surveillance of multidrug-resistant S. Goldcoast from a global "One Health" perspective is urgently needed to facilitate monitoring the spread of the antimicrobial resistant high-risk clones.

Global Phylogeography and Genomic Epidemiology of Carbapenem-Resistant blaOXA-232-Carrying Klebsiella pneumoniae Sequence Type 15 Lineage.

Prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) has compromised antimicrobial efficacy against severe infections worldwide. To monitor global spread, we conducted a comprehensive genomic epidemiologic study comparing sequences from 21 blaOXA-232-carrying CRKP isolates from China with K. pneumoniae sequence type (ST) 15 strains from 68 countries available in GenBank. Phylogenetic and phylogeographic analyses revealed all blaOXA-232-carrying CRKP isolates belonged to ST15 lineage and exhibited multidrug resistance. Analysis grouped 330 global blaOXA-232-carrying ST15 CRKP strains into 5 clades, indicating clonal transmission with small genetic distances among multiple strains. The lineage originated in the United States, then spread to Europe, Asia, Oceania, and Africa. Most recent common ancestor was traced back to 2000; mutations averaged ≈1.7 per year per genome. Our research helps identify key forces driving global spread of blaOXA-232-carrying CRKP ST15 lineage and emphasizes the importance of ongoing surveillance of epidemic CRKP.

Genomic epidemiology of mcr carrying multidrug-resistant ST34 Salmonella enterica serovar Typhimurium in a one health context: The evolution of a global menace.

The rapid global dissemination of Salmonella enterica sequence type 34 (ST34) has sparked significant concern due to its resistance to critical antimicrobials and its ability to spread across various sectors. In order to investigate the evolution and transmission dynamics of this epidemic clonal lineage, as well as the horizontal transfer of mcr-carrying plasmids within the One Health framework, we conducted a comprehensive genomic epidemiological study. This study focused on the 11 mcr-carrying S. enterica isolates obtained from clinical settings in China, while also considering 2337 publicly available genomes of mcr-carrying S. enterica collected from 20 countries and diverse sources spanning over a 22-year period. Among the mcr-positive Salmonella isolates, ST34 was found to be the predominant lineage, comprising 30.12 % (704/2337) of the total collection. These isolates were identified as either serovar Typhimurium or its monophasic variant, which were obtained from both clinical and non-clinical sources. Phylogeographic analyses traced the global spread of the mcr-carrying ST34 lineage, which was divided into three distinct clusters, with 83.10 % of them carrying mcr-1 or/and mcr-9 genes. Notably, the mcr-1 positive ST34 isolates were primarily found in China (190/298, 63.76 %), with only four from the United States. Conversely, mcr-9 positive ST34 isolates were predominantly identified in the United States (261/293, 89.08 %), while none were observed in China. The mcr-1 positive ST34 isolates was predicted to have originated from clinical sources in United Kingdom, whereas mcr-9 positive ST34 isolates was likely derived from environmental sources in Germany. The most recent common ancestor for mcr-1 and mcr-9 carrying ST34 S. enterica was estimated to have emerged around 1983 and 1951. These findings provided thorough and intuitive insights into the intercontinental spread of mcr-carrying S. enterica ST34 lineage in a One Health context. Ongoing surveillance is crucial for effectively monitoring the worldwide dissemination of this multidrug-resistant high-risk clone.

Global emergence of carbapenem-resistant Klebsiella pneumoniae co-carrying multiple carbapenemases.

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) co-carrying multiple carbapenemases is complicating clinical treatment. This study aimed to investigate the global dissemination trends of CRKP strains that co-carry multiple carbapenemases. The CRKP isolate KP424 co-carrying blaNDM-1 and blaKPC-2, recovered from a stool specimen, was identified by the NG-Test Carba 5 test, and the genome sequence was further determined by using Nanopore MinION and Illumina NovaSeq 6000 technologies. The genome sequences of the CRKP strains carrying multiple carbapenemase genes were further retrieved from the NCBI GenBank database. Thirteen antimicrobial resistance genes, including blaNDM-1 and blaKPC-2, have been identified in KP424, with blaNDM-1 and blaKPC-2 located on different plasmids. In total, 832 genome sequences of CRKP strains co-carrying two carbapenemase genes were retrieved from the NCBI database. Strains carrying both blaNDM and blaOXA-48-like accounted for 665 (79.9 %) of the total strains, ranking first, and those carrying both blaKPC and blaNDM accounted for 103 (12.4 %), ranking second. The prevalence of CRKP strains co-carrying two carbapenemase genes increased significantly over time, from 0.40 % in 2010 to 9.67 % in 2021. The proportion of strains carrying both blaKPC and blaNDM has also increased, from 0.00 % in 2010 to 4.40 % in 2021. The strains carrying both blaKPC and blaNDM had the highest prevalence (66.7 %, 52/78) in China, while those carrying both blaNDM and blaOXA-48-like had the highest prevalence worldwide. Multiple-carbapenemase producers pose a great threat to public health; further research on the mechanisms underlying multiple carbapenemase gene occurrence is required to prevent their global dissemination.

Global population structure and genomic surveillance framework of carbapenem-resistant Salmonella enterica.

Due to the frequent international and intercontinental transmission of multidrug-resistant bacteria, it is imperative to understand the epidemiology, phylogeography, and population structure of carbapenem-resistant Salmonella enterica (CRSE) across the globe. During the period of 2015-2022, two blaNDM-carrying S. enterica strains were recovered from 3695 Salmonella strains in four hospitals in China. The global phylogenetic framework and geographical distribution of CRSE were defined by our recently updated bacterial whole genome sequence typing and source tracking database BacWGSTdb 2.0 to measure the diversity and evolutionary relatedness in context with epidemiological metadata. Phylogeny for all carbapenemase gene-harboring plasmids in S. enterica based on the pairwise Mash differences was also constructed to evaluate the potential transmission of these plasmids in a global context. A large-scale phylogenetic analysis grouped global CRSE into nine distinct clades. The small genetic distance (< 20 SNPs) between 198 pairs of CRSE suggested the presence of clonal transmission. Global CRSE have significant geographical variations, which was associated with the clonal lineages and carbapenemase genes. Carbapenemase gene-carrying plasmids with a high degree of similarity have surfaced in various hosts and countries. The widespread of multiple-replicon plasmids that offer a great capacity to accommodate multiple antimicrobial resistance genes is continuously enhancing the potential risk of CRSE isolates to propagate globally. Both clonal spread of strains and horizontal transfer of carbapenemase gene-harboring plasmids contribute to the global dissemination of CRSE. Our findings on the worldwide spread and transmission dynamics of this emerging bacterium has increased the knowledge of its global epidemics. Continued epidemiological surveillance is necessary to prevent global outbreak of multidrug-resistant Salmonella infections.

Genomic Insights into the Colistin Resistant mcr-Carrying Escherichia coli Strains in a Tertiary Hospital in China.

Colistin is an important antimicrobial agent in the treatment of infections caused by multidrug resistant (MDR) Gram-negative bacteria. The horizontal transfer of mobile colistin resistance gene (mcr) poses a major threat to the public health worldwide. In this study, a total of thirteen mcr-carrying Escherichia coli (MCREC) strains were recovered from a tertiary hospital in Zhejiang, China, between 2016 and 2019. The minimum inhibitory concentration (MIC) of antimicrobial agents, epidemiological characteristics, and transmission dynamics of mcr-carrying isolates were analyzed using antimicrobial susceptibility testing, whole-genome sequencing, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), and southern blotting analysis. All strains were discovered to be resistant to colistin, and the majority displayed MDR phenotype. However, none of the 13 MCREC strains were resistant to carbapenems. The 13 MCREC isolates were divided into 10 different STs, including ST744, ST156, ST453, ST410, ST57, ST131, ST7034, ST2599, ST457, and ST13239, in which ST13239 was discovered for the first time. Based on core genome single nucleotide polymorphism (cgSNP) analysis, no clear epidemiological link was discovered in these strains with the exception of EC2118 and EC3807, which differ by just one SNP. A total of 35 antimicrobial resistance genes which can be divided into 14 classes were identified from the 13 MCREC isolates. According to S1-PFGE and southern blotting analyses, all 13 MCREC strains had plasmid-mediated mcr-1, and nine of them carried conjugative plasmids. In conclusion, our study revealed the emergence and dissemination of colistin-resistant E. coli isolates carrying mcr-1 in a Chinese hospital, which poses a potential risk to anti-infective therapy. More efforts should be taken to monitor the prevalence of mcr-1-carrying bacteria in China.

Clinical Features, Management and Maternal-Infant Prognosis in Patients with Complete Uterine Rupture in the Second and Third Trimester of Pregnancy.

Objectives: Our study aimed to investigate the clinical features, management, and maternal-infant prognosis in patients with complete uterine rupture in the second and third trimester of pregnancy. Methods: A total of 15 patients with complete uterine rupture in their second and third trimester of pregnancy who were admitted to our hospital between January 2012 and December 2020 were included in our study. The patients enrolled were divided into the scar group (11 patients) and the non-scar group (4 patients) according to the existence or absence of a uterine scar. The general data, clinical characteristics and follow-up results in the 2 groups were compared. Results: There was no significant difference in age, pregnancy duration or delivery cycle between the 2 groups (P > .05). The incidence of original scar rupture in the scar group was significantly higher than in the non-scar group (P > .05). No significant difference was found in clinical characteristics between the scar and the non-scar groups (P > .05). The most common clinical features included abdominal pain, inability to lie flat, hemorrhagic shock, prenatal vaginal bleeding and uterine rupture, mostly occurring in the lower segments of the uterus and cervix. A total of 3 patients were misdiagnosed as having surgical disease. After completing relevant examinations, the uterine rupture was repaired surgically; the patients were discharged after blood transfusion, and their condition resolved. In all, 3 patients in the non-scar group and 1 patient in the scar group were transferred to the intensive care unit (ICU). All 15 patients were discharged after treatment. Follow-up was completed by all patients for 12 to 36 months, with an average follow-up time of 23.09 ± 2.19 months. Of the 15 patients, 2 underwent induced abortion after 24 months due to unplanned pregnancy. A 5-minute Apgar score of ≤7 in the scar group was higher than that in the non-scar group, but the difference was not statistically significant (P > .05). Perinatal mortality in the 15 patients was 40.00% (6/15). Conclusion: The most common clinical features in patients with complete uterine rupture in the second and third trimester of pregnancy included abdominal pain, inability to lie flat, hemorrhagic shock, prenatal vaginal bleeding and uterine rupture, mostly occurring in the lower segments of the uterus and cervix. In addition, a remarkably worse maternal-infant prognosis was seen in patients with complete uterine rupture in the second and third trimester of scarless pregnancy compared with patients with complete uterine rupture in the second and third trimester of scarred pregnancy.

Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids.

Metagenomic next-generation sequencing (mNGS) enables comprehensive pathogen detection and has become increasingly popular in clinical diagnosis. The distinct pathogenic traits between strains require mNGS to achieve a strain-level resolution, but an equivocal concept of 'strain' as well as the low pathogen loads in most clinical specimens hinders such strain awareness. Here we introduce a metagenomic intra-species typing (MIST) tool (https://github.com/pandafengye/MIST), which hierarchically organizes reference genomes based on average nucleotide identity (ANI) and performs maximum likelihood estimation to infer the strain-level compositional abundance. In silico analysis using synthetic datasets showed that MIST accurately predicted the strain composition at a 99.9% average nucleotide identity (ANI) resolution with a merely 0.001× sequencing depth. When applying MIST on 359 culture-positive and 359 culture-negative real-world specimens of infected body fluids, we found the presence of multiple-strain reached considerable frequencies (30.39%-93.22%), which were otherwise underestimated by current diagnostic techniques due to their limited resolution. Several high-risk clones were identified to be prevalent across samples, including Acinetobacter baumannii sequence type (ST)208/ST195, Staphylococcus aureus ST22/ST398 and Klebsiella pneumoniae ST11/ST15, indicating potential outbreak events occurring in the clinical settings. Interestingly, contaminations caused by the engineered Escherichia coli strain K-12 and BL21 throughout the mNGS datasets were also identified by MIST instead of the statistical decontamination approach. Our study systemically characterized the infected body fluids at the strain level for the first time. Extension of mNGS testing to the strain level can greatly benefit clinical diagnosis of bacterial infections, including the identification of multi-strain infection, decontamination and infection control surveillance.

Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections.

Antibiotic resistance is spreading rapidly around the world and seriously impeding efforts to control microbial infections. Although nucleic acid testing is widely deployed for the detection of antibiotic resistant bacteria, the current techniques-mainly based on polymerase chain reaction (PCR)-are time-consuming and laborious. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance (AMR). The CRISPR-Cas system is an adaptive immune system found in many prokaryotes that presents attractive opportunities to target and edit nucleic acids with high precision and reliability. Engineered CRISPR-Cas systems are reported to effectively kill bacteria or even revert bacterial resistance to antibiotics (resensitizing bacterial cells to antibiotics). Strategies for combating antimicrobial resistance using CRISPR (i.e., Cas9, Cas12, Cas13, and Cas14) can be of great significance in detecting bacteria and their resistance to antibiotics. This review discusses the structures, mechanisms, and detection methods of CRISPR-Cas systems and how these systems can be engineered for the rapid and reliable detection of bacteria using various approaches, with a particular focus on nanoparticles. In addition, we summarize the most recent advances in applying the CRISPR-Cas system for virulence modulation of bacterial infections and combating antimicrobial resistance.

Comprehensive Analysis of the Expression, Prognosis, and Biological Significance of OVOLs in Breast Cancer.

BACKGROUND: The study aimed to investigate the expression of OVOLs in breast cancer (BRCA) tissues and their value in prognosis. METHODS: ONCOMINE was used to analyze the expressions of OVOL1, OVOL2, and OVOL3 mRNA between BRCA tissues and normal breast tissues. The Wilcoxon rank sum test and t-test were used to assess the expression of OVOLs between BRCA tissues and unpaired/paired normal breast tissues. GEPIA and ROC curves were used to analyze the relationship between OVOLs expression and clinical pathological stage. Kaplan-Meier plotter was used to analyze prognosis. cBioPortal was used to analyze the mutation of OVOLs. GEPIA was used to analyze the co-expression of OVOLs. GO and KEGG analyses were performed by the DAVID software to predict the function of OVOLs co-expression genes. RESULTS: The expression of OVOL1/2 was significantly higher in BRCA tissues than in normal breast tissues. The OVOL3 expression correlated with tumor stage. The AUC of OVOLs was 0.757, 0.754, and 0.537, respectively. OVOL1 high expression was associated with shorter overall survival (HR: 1.48; 95% CI: 1.07-2.04; P=0.018). The OVOLs were associated with pathways including axon guidance, thyroid hormone signaling pathway, and ubiquinone and other terpenoid-quinone biosynthesis. CONCLUSION: OVOL1 is a new potential marker of prognosis in BRCA, and OVOL1/2 are potential therapeutic targets in BRCA.

High-resolution genome-wide association study and genomic prediction for disease resistance and cold tolerance in wheat.

KEY MESSAGE: High-resolution genome-wide association study (GWAS) facilitated QTL fine mapping and candidate gene identification, and the GWAS based genomic prediction models were highly predictive and valuable in wheat genomic breeding. Wheat is a major staple food crop and provides more than one-fifth of the daily calories and dietary proteins for humans. Genome-wide association study (GWAS) and genomic selection (GS) for wheat stress resistance and tolerance related traits are critical to understanding their genetic architecture for improvement of breeding selection efficiency. However, the insufficient marker density in previous studies limited the utility of GWAS and GS in wheat genomic breeding. Here, we conducted a high-resolution GWAS for wheat leaf rust (LR), yellow rust (YR), powdery mildew (PM), and cold tolerance (CT) by genotyping a panel of 768 wheat cultivars using genotyping-by-sequencing. Among 153 quantitative trait loci (QTLs) identified, 81 QTLs were delimited to ≤ 1.0 Mb intervals with three validated using bi-parental populations. Furthermore, 837 stress resistance-related genes were identified in the QTL regions with 12 showing induced expression by YR and PM pathogens. Genomic prediction using 2608, 4064, 3907, and 2136 pre-selected SNPs based on GWAS and genotypic correlations between the SNPs showed high prediction accuracies of 0.76, 0.73, and 0.78 for resistance to LR, YR, and PM, respectively, and 0.83 for resistance to cold damage. Our study laid a solid foundation for large-scale QTL fine mapping, candidate gene validation and GS in wheat.

Knockdown of sterol O-acyltransferase 1 (SOAT1) suppresses SCD1-mediated lipogenesis and cancer procession in prostate cancer.

Prostate cancer (PCa) is one of the most fatal malignant tumors that occurs in the prostate epithelium, especially in older men, the mortality of which ranks sixth among all cancer-related deaths. It has been urgently needed to elucidate the pathogenesis of PCa and provide promising therapeutic targets for PCa treatment. The Sterol O-acyltransferase 1 (SOAT1), cholesterol metabolism enzyme, was widely expressed in various cancer tissues, resulting in cancer progression. SOAT1 has been demonstrated to be highly expressed in prostate cancer tissues, whereas the underlying mechanism has not been elucidated. Herein, we found the expression of SOAT1 was elevated in human PCa tissues, which demonstrated SOAT1 level was correlated with lymph node metastasis (p = 0.006), clinical stage (p = 0.032), grading (p = 0.036), and Gleason score (p = 0.030) of PCa patients. In addition, we revealed that SOAT1 promoted proliferation and liposynthesis of PCa cells by targeting Stearoyl-CoA Desaturase 1 (SCD1). Our data further confirmed that SCD1 overexpression reversed the proliferation and liposynthesis defects caused by SOAT1 depletion in PCa cells, however, SOAT1 depletion inhibited tumor growth of PCa cells in mice. We further found SOAT1 contributed to the progression of PCa via SREBF1 pathway. Taken together, our data revealed the mechanism underlying SOAT1 promoting PCa progression in vitro and in vivo.

Artificial selection in breeding extensively enriched a functional allelic variation in TaPHS1 for pre-harvest sprouting resistance in wheat.

Pre-harvest sprouting (PHS) causes significant losses in wheat yield and quality worldwide. Previously, we cloned a PHS resistance gene, TaPHS1, and identified two causal mutations for reduced seed dormancy (SD) and increased PHS susceptibility. Here we identified a novel allelic variation of C to T transition in 3'-UTR of TaPHS1, which associated with reduced SD and PHS resistance. The T allele occurred in wild wheat progenitors and was likely the earliest functional mutation in TaPHS1 for PHS susceptibility. Allele frequency analysis revealed low frequency of the T allele in wild diploid and tetraploid wheat progenitors, but very high frequency in modern wheat cultivars and breeding lines, indicating that artificial selection quickly enriched the T allele during modern breeding. The T allele was significantly associated with short SD in both T. aestivum and T. durum, the two most cultivated species of wheat. This variation together with previously reported functional sequence variations co-regulated TaPHS1 expression levels and PHS resistance in different germplasms. Haplotype analysis of the four functional variations identified the best PHS resistance haplotype of TaPHS1. The resistance haplotype can be used in marker-assisted selection to transfer TaPHS1 to new wheat cultivars.

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat.

Wheat (Triticum aestivum) is a major staple food crop worldwide. Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population. We conducted a large-scale genome-wide association study (GWAS) using a panel of 768 wheat cultivars that were genotyped with 327 609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci (QTLs) for 12 traits under 7 environments. Among them, 273 QTLs were delimited to ≤1.0-Mb intervals and 7 of them are either known genes (Rht-D, Vrn-B1, and Vrn-D1) that have been cloned or known QTLs (TaGA2ox8, APO1, TaSus1-7B, and Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three bi-parental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits. Large r2 values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable. Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation for large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.