Genetic Characteristics
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2022 ◽  
Vol 2022 ◽  
pp. 1-9
Author(s):  
Samira Zamani ◽  
Anis Mohammadi ◽  
Bahareh Hajikhani ◽  
Parnaz Abiri ◽  
Maryam Fazeli ◽  
...  

The spread of mupirocin-resistant Staphylococcus aureus strains in hospitals and communities is a universal challenge. Limited data is available on the genetic features of high-level mupirocin resistant- (HLMUPR-) S. aureus isolates in Tehran. In the present research, we investigated 48 high-level mupirocin resistance S. aureus by antimicrobial activity, virulence analysis, biofilm formation, multilocus sequence typing (MLST), and staphylocoagulase (SC) typing. All the HLMUPR strains were positive for mupA gene. The frequency of multidrug resistance was 97.9%. Twenty-one (43.8%) were toxinogenic with 14 producing pvl (29.2%), 5 tst (10.4%), and two eta (4.2%). Among the HLMUPR isolates, biofilm production was detected in 45 (89.6%) isolates with complete dominance clfB, clfA genes, and a noticeably high frequency fnbA (95.8%), followed by fnbB (93.8%), eno and icaD (each 83.3%), sdrC (81.3%), ebps (79.2%), icaA (75%), sdrD (66.7%), fib (60.4%), sdrE (50%), cna (41.7%), and bap (4.2%). Coagulase typing distinguished isolates into four genotypic patterns including III (50%), II (27.1%), and type IVa (22.9%). A total of three clonal complexes (CCs) and 4 sequence types (STs) including CC/ST22 as the most prevalent (52.1%), CC8/ST239 (20.8%), CC/ST8 (16.7%), and CC/ST5 (10.4%) were identified in current work. According to our analysis, nonbiofilm producer isolates belonged to CC8/ST239 (6.3%) and CC/ST8 (4.2%). Fusidic acid-resistant isolates belonged to CC/ST45 ( n = 3 ) and CC8/ST239 ( n = 1 ). Observations highlighted the circulation of the CC/ST22 HLMUPR S. aureus strains with strong biofilm-production ability in our hospitals, indicating the possibility of transmission of this type between community and hospital.


Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 137
Author(s):  
Tatyana Markova ◽  
Vladimir Kenis ◽  
Evgeniy Melchenko ◽  
Darya Osipova ◽  
Tatyana Nagornova ◽  
...  

The significant variability in the clinical manifestations of COL2A1-associated skeletal dysplasias makes it necessary to conduct a clinical and genetic analysis of individual nosological variants, which will contribute to improving our understanding of the pathogenetic mechanisms and prognosis. We presented the clinical and genetic characteristics of 60 Russian pediatric patients with type II collagenopathies caused by previously described and newly identified variants in the COL2A1 gene. Diagnosis confirmation was carried out by new generation sequencing of the target panel with subsequent validation of the identified variants using automated Sanger sequencing. It has been shown that clinical forms of spondyloepiphyseal dysplasias predominate in childhood, both with more severe clinical manifestations (58%) and with unusual phenotypes of mild forms with normal growth (25%). However, Stickler syndrome, type I was less common (17%). In the COL2A1 gene, 28 novel variants were identified, and a total of 63% of the variants were found in the triple helix region resulted in glycine substitution in Gly-XY repeats, which were identified in patients with clinical manifestations of congenital spondyloepiphyseal dysplasia with varying severity, and were not found in Stickler syndrome, type I and Kniest dysplasia. In the C-propeptide region, five novel variants leading to the development of unusual phenotypes of spondyloepiphyseal dysplasia have been identified.


Author(s):  
Tatsuhiro Kato ◽  
Yong Guo ◽  
Reiko Fujimura ◽  
Takamichi Nakamura ◽  
Tomoyasu Nishizawa ◽  
...  

The genome sequence of Acidithiobacillus ferrooxidans strain NFP31, which is a chemolithoautotrophic iron-oxidizing bacterium that inhabits acidified volcanic deposits on Mount Oyama, Miyake Island (Miyake-jima), Japan, was determined to identify the genetic characteristics associated with pioneer microbes in newly placed pyroclastic deposits.


2022 ◽  
Vol 19 (2) ◽  
pp. em350
Author(s):  
Aygerim Zhuzzhasarova ◽  
Dinagul Bayesheva ◽  
Nurshay Azimbaeva ◽  
Manar Smagul ◽  
Gauhar Nusupbaeva ◽  
...  

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 136
Author(s):  
Flavio De Angelis ◽  
Marco Romboni ◽  
Virginia Veltre ◽  
Paola Catalano ◽  
Cristina Martínez-Labarga ◽  
...  

This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first–third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops.


2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Yongjuan Liu ◽  
Jingyi Zhou ◽  
Guangquan Ji ◽  
Yupeng Gao ◽  
Chunyan Zhang ◽  
...  

AbstractRecombination plays important roles in the genetic diversity and evolution of Enterovirus A71 (EV-A71). The phylogenetics of EV-A71 in mainland China found that one strain DL71 formed a new subgenotype C6 with unknown origin. This study investigated the detailed genetic characteristics of the new variant. DL71 formed a distinct cluster within genotype C based on the genome and individual genes (5′UTR, VP4, VP1, 2A, 2B, 2C, 3D, and 3′UTR). The average genetic distances of the genome and individual genes (VP3, 2A, 2B, 2C, 3A, 3C, and 3D) between DL71 and reference strains were greater than 0.1. Nine recombination events involving smaller fragments along DL71 genome were detected. The strains Fuyang-0805a (C4) and Tainan/5746/98 (C2) were identified as the parental strains of DL71. In the non-recombination regions, DL71 had higher identities with Fuyang-0805a than Tainan/5746/98, and located in the cluster with C4 strains. However, in the recombination regions, DL71 had higher identities with Tainan/5746/98 than Fuyang-0805a, and located in the cluster with C2 strains. Thus, DL71 was a novel multiple inter-subgenotype recombinant derived from the dominant subgenotype C4 and the sporadic subgenotype C2 strains. Monitoring the emergence of new variants by the whole-genome sequencing remains essential for preventing disease outbreaks and developing new vaccines.


Author(s):  
Bingjie Wang ◽  
Fen Pan ◽  
Dingding Han ◽  
Wantong Zhao ◽  
Yingying Shi ◽  
...  

As an important member of the Klebsiella pneumoniae complex, Klebsiella variicola is poorly studied as an emerging human pathogen. We, for the first time, report a unique K. variicola isolated from a pediatric patient in China.


2022 ◽  
Vol 98 (6) ◽  
pp. 627-638
Author(s):  
I. A. Lapovok ◽  
P. B. Baryshev ◽  
D. V. Saleeva ◽  
A. A. Kirichenko ◽  
A. V. Shlykova (Murzakova) ◽  
...  

Introduction. The aim of the study was to use comparative analysis for assessing efficiency of detection and confirmation of dual HIV infection, using conventional population sequencing (PS) and next generation sequencing (NGS) for an HIV-1 pol gene fragment, which encompasses protease and partially reverse transcriptase (positions 2253–3368).Materials and methods. The study was performed on intersubtype dual HIV infection model samples containing viruses of HIV-1 subtype B, sub-subtype A6 and recombinant form CRF63_02A1. Viruses were mixed pairwise in proportions from 10 to 90% to obtain 3 groups of model samples: CRF63vsB, CRF63vsA6, and A6vsB. The nucleotide sequences obtained by using PS and NGS technologies having 5, 10, 15, and 20% sensitivity thresholds for minor virus variants (NGS5–NGS20, respectively) were used to estimate the number of degenerate nucleotides or the degenerate base (DB) count and the number of synonymous mutations (SM) or the SM count. The fragment of the studied region (positions 2725–2981) was used for the analysis of operational taxonomic units.Results. The application of NGS5 proved highly efficient for detection of dual HIV infection in the model samples. The statistically significant (p < 0.01) increase in DB and SM counts was demonstrated by NGS5 compared to PS. As a result, NGS5 helped detect dual HIV infection in 25 out of 27 model samples, while with PS it was detected only in 15 samples. The analysis of operational taxonomic units confirmed dual HIV infection in all the groups of model samples.Discussion. The efficiency of detection and confirmation of dual HIV infection depends both on the content of each virus in the sample and on genetic characteristics of these viruses. Conclusion. Using NGS genetic testing in routine practice will be instrumental for efficient identification of genetic characteristics of infectious agents and for thorough analysis of the epidemiological situation.


2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Qiang-Wei Wang ◽  
Wei-Wei Lin ◽  
Yong-Jian Zhu

Abstract Background Several studies have shown that members of the tumor necrosis factor (TNF) family play an important role in cancer immunoregulation, and trials targeting these molecules are already underway. Our study aimed to integrate and analyze the expression patterns and clinical significance of TNF family-related genes in gliomas. Methods A total of 1749 gliomas from 4 datasets were enrolled in our study, including the Cancer Genome Atlas (TCGA) dataset as the training cohort and the other three datasets (CGGA, GSE16011, and Rembrandt) as validation cohorts. Clinical information, RNA expression data, and genomic profile were collected for analysis. We screened the signature gene set by Cox proportional hazards modelling. We evaluated the prognostic value of the signature by Kaplan–Meier analysis and timeROC curve. Gene Ontology (GO) and Gene set enrichment analysis (GSEA) analysis were performed for functional annotation. CIBERSORT algorithm and inflammatory metagenes were used to reveal immune characteristics. Results In gliomas, the expression of most TNF family members was positively correlated. Univariate analysis showed that most TNF family members were related to the overall survival of patients. Then through the LASSO regression model, we developed a TNF family-based signature, which was related to clinical, molecular, and genetic characteristics of patients with glioma. Moreover, the signature was found to be an independent prognostic marker through survival curve analysis and Cox regression analysis. Furthermore, a nomogram prognostic model was constructed to predict individual survival rates at 1, 3 and 5 years. Functional annotation analysis revealed that the immune and inflammatory response pathways were enriched in the high-risk group. Immunological analysis showed the immunosuppressive status in the high-risk group. Conclusions We developed a TNF family-based signature to predict the prognosis of patients with glioma.


2022 ◽  
Vol 11 ◽  
Author(s):  
Xin-tao Yu ◽  
Lei Yu ◽  
Xin Du ◽  
Zhen Yu ◽  
Xing-guo Yang ◽  
...  

BackgroundOur study investigated a special series of thymoma with autoimmune hepatitis and myocarditis and tried to reveal the gene expression profiles of this series of thymoma.MethodsFrom 2011 to 2019, a total of 13 special thymoma patients presented with autoimmune hepatitis and myocarditis, accounting for about 1.26% of thymoma patients undergoing surgery in Beijing TongRen Hospital. Clinical data were retrospectively collected. All samples were harvested during surgical procedures, and analyzed to identify changes in gene expression using the CapitalBio mRNA microarray analysis, the Whole exome sequencing analysis (WES), qPCR and immunohistochemistry (IHC) tools.ResultsAfter surgery, patient symptoms were relieved gradually. Levels of lactate dehydrogenase (LDH), creatine kinase MB (CK-MB), aspartate transaminase (AST), and alanine amiotransferase (ALT) increased to some extent within 1 to 3 months after surgery, and fluctuated, and then, gradually decreased close to normal within 6 months after surgery. Enrichment analysis of Kyoto Genome and Genome Encyclopedia (KEGG) pathway was performed and enrichment results were visualized. It indicated that gene expression of 5 signaling pathways, including cell cycle and p53 signaling pathway, were generally abnormal. P53 expression was up-regulated in all tumor tissues. However, IHC and qPCR analysis showed that there was no significant difference in p21 expression between normal and tumor tissue. Results of WES showed that only one driver gene-MDM4 amplified 4 fold in 53.2% thymoma cells. Further qPCR and IHC analysis confirmed the up-regulation of the expression of p53 and mdm4 in 13 thymoma patients with autoimmune hepatitis and myocarditis.ConclusionOur study reveals the clinical and genetic characteristics of thymoma patients with autoimmune hepatitis and myocarditis. For this special category of thymoma, the up-regulation of p53 and mdm4 plays an important role in the occurrence of thymoma and autoimmune hepatitis/myocarditis.


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