Genomic Features Research Articles

CT-guided Coaxial Lung Biopsy: Number of Cores and Association with Complications.

Background Percutaneous CT-guided lung core-needle biopsy is a frequently performed and generally safe procedure. However, with advances in the management of lung cancer, there is a need for a greater amount of tissue for tumor genomic profiling and characterization. Purpose To determine whether the number of core samples obtained with percutaneous CT-guided lung biopsy is associated with postprocedural complications. Materials and Methods This retrospective study included consecutive patients who underwent percutaneous CT-guided coaxial lung core-needle biopsy for suspected primary lung cancer between November 2012 and August 2023 at an academic tertiary referral hospital. Patient data from medical records were collected, including demographics, lesion size and distance from pleura, and number of obtained biopsy samples. Postprocedural complications of pneumothorax, chest tube placement, perilesional hemorrhage, and hemoptysis were recorded. Multivariable logistic regression models were used to assess whether the number of cores was a predictive factor for lung biopsy complications. Results A total of 827 patients (mean age, 70.9 years ± 9.6 [SD]; 474 [57.3%] female patients) were included. The median lesion size was 22 mm (IQR, 15-34 mm), with 517 of 827 (62.5%) patients diagnosed with lung adenocarcinoma. Pneumothorax was noted in 171 of 827 (20.7%) patients, with a chest tube placed in 32 of 827 (3.9%), perilesional hemorrhage in 353 of 827 (42.7%), and hemoptysis in 20 of 827 (2.4%) patients. The median number of samples obtained was four (range, one to 12). Multivariable analysis showed no evidence of an association between the number of core samples obtained and any complications: pneumothorax (coefficient, -0.02; P = .81), chest tube (coefficient, 0.18; P = .26), perilesional hemorrhage (coefficient, -0.03; P = .63), or hemoptysis (coefficient, -0.10; P = .60). Conclusion In patients suspected of having lung cancer who underwent percutaneous CT-guided coaxial lung core biopsy, there was no evidence of an association between the number of core biopsy samples obtained and any postprocedural complications. © RSNA, 2024 See also the editorial by Zuckerman in this issue.

Exploring common bean's defense arsenal: Genome-wide characterization of PR-1 gene family and its transcriptional response to Colletotrichum lindemuthianum inoculation

Pathogenesis-related Protein 1 (PR-1) plays a crucial role in plant defense responses, particularly against fungal pathogens. Despite its significance, comprehensive studies characterizing this gene family in the common bean (Phaseolus vulgaris) are currently lacking. Therefore, the objective of this study was to conduct genomic mining and characterization of the PR-1 in common bean (PvPR-1) genome. Additionally, we assessed the transcriptional expression of all its isoforms in response to inoculation with the fungus Colletotrichum lindemuthianum. This evaluation was performed on leaf tissue samples obtained from both sensitive (Rosinha) and resistant (Africano 4) common bean varieties at 24-, 48-, and 96-hours post inoculation. Thirteen PvPR-1 genes were consistently identified, forming two major clusters across the clustering analyses. Physicochemical characterization indicated that the PvPR-1 proteins are predominantly basic, hydrophilic, and extracellularly localized. Moreover, their promoter regions contain putative cis-regulatory elements that respond to a broad spectrum of plant hormones, including jasmonic acid, gibberellin, and ethylene, which are key regulators of both biotic and abiotic stress responses. This discovery implies a multifaceted role for the studied proteins in common bean physiology. KEGG pathway analysis implicated PvPR-1 proteins in hormonal signaling (corroborating the anchored cis-regulatory elements) and plant-pathogen interaction networks. Secondary structure evaluation revealed the predominance of α-helices and coiled structures within these proteins. Subsequent 3D modeling demonstrated a conserved ‘α-β-α’ sandwich architecture characterized by a central cavity. This structural motif suggests potential functional versatility, particularly in pathogen recognition and responses. Additionally, the study provided insight into the potential interactions of PvPR-1 with Chitinase II (PR-3) and Rab-18, as suggested by the STRING platform. Temporal differences in PvPR-1 gene expression were observed between the common bean contrasting varieties following C. lindemuthianum inoculation. Africano-4, the resistant one, showed a higher abundance of up-regulated and constitutively expressed PvPR-1 transcripts compared to its sensitive counterpart (Rosinha), indicating a more effective role of this gene family against the pathogen. Furthermore, based on PCA analyses and interaction networks of differentially expressed genes, three key targets within the PvPR-1 family (PvPR-1-4, PvPR-1-5, and PvPR-1-10) emerged as promising candidates for future functional characterization. These molecular actors displayed differential transcriptional patterns between the studied varieties without compromising the transcript abundance of PvPR-1 protein synthesis in the resistant one. Consequently, they may represent key components of resistance mechanisms that contribute to the differentiation between the two organisms. These findings deepen our understanding of PvPR-1 genes and their roles in common bean defense responses. They also emphasized the potential of PvPR-1 genes as candidates for breeding stress-resistant common bean varieties, which are crucial for bolstering crop resilience to environmental adversities.

Genomes and epigenomes of matched normal and tumor breast tissue reveal diverse evolutionary trajectories and tumor-host interactions.

Normal tissues adjacent to the tumor (NATs) may harbor early breast carcinogenesis events driven by field cancerization. Although previous studies have characterized copy-number (CN) and transcriptomic alterations, the evolutionary history of NATs in breast cancer (BC) remains poorly characterized. Utilizing whole-genome sequencing (WGS), methylation profiling, and RNA sequencing (RNA-seq), we analyzed paired germline, NATs, and tumor samples from 43 individuals with BC in Hong Kong (HK). We found that single-nucleotide variants (SNVs) were common in NATs, with one-third of NAT samples exhibiting SNVs in driver genes, many of which were present in paired tumor samples. The most frequently mutated genes in both tumor and NAT samples were PIK3CA, TP53, GATA3, and AKT1. In contrast, large-scale aberrations such as somatic CN alterations (SCNAs) and structural variants (SVs) were rarely detected in NAT samples. We generated phylogenetic trees to investigate the evolutionary history of paired NAT and tumor samples. They could be categorized into tumor only, shared, and multiple-tree groups, the last of which is concordant with non-genetic field cancerization. These groups exhibited distinct genomic and epigenomic characteristics in both NAT and tumor samples.Specifically, NAT samples in the shared-tree group showed higher number of mutations, while NAT samples belonging to the multiple-tree group showed a less inflammatory tumor microenvironment (TME), characterized by a higher proportion ofregulatory Tcells (Tregs) and lower presence of CD14 cell populations. In summary, our findings highlight the diverse evolutionary history in BC NAT/tumor pairs and the impact of field cancerization and TME in shaping the genomic evolutionary historyof tumors.

Genomic characterization of mucinous adenocarcinoma of the cervix

Genomic characterization of mucinous adenocarcinoma of the cervix

Development of a MALDI-TOF MS model for differentiating haemorrhagic septicaemia-causing strains of Pasteurella multocida from other capsular groups.

Pasteurella multocida capsular types A, D, and F cause disease in many animal hosts, including bovine respiratory disease in cattle, which is one of the most globally significant animal diseases. Additionally, P. multocida capsular types B and E cause haemorrhagic septicaemia, a devastating disease primarily of cattle, water buffalo, and bison that develops rapidly with high mortality. Haemorrhagic septicaemia mostly occurs in developing countries and has potential to emerge elsewhere in the world. The diagnosis of haemorrhagic septicaemia currently requires recognition of compatible gross or histologic lesions and serotyping or molecular characterization of strains. In this study, we performed genomic characterization of 84 P. multocida strains, which were then used to develop and validate a matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) biomarker-based method for differentiating non-haemorrhagic septicaemia strains of P. multocida from haemorrhagic septicaemia-causing strains. Haemorrhagic septicaemia strain types B:2,5, E:2,5, and B:3,4 were used to maximize diversity. Three automated classification models were generated and then used to develop an assisted model, which utilized two peaks (6419 and 7729 m/z) to accurately differentiate non-haemorrhagic septicaemia-causing strains from haemorrhagic septicaemia-causing strains of P. multocida. The assisted model performed with 98.2 % accuracy for non-haemorrhagic septicaemia strains, 100 % accuracy for classic B:2,5 and E:2,5 strains, and 84.4 % accuracy for combined haemorrhagic septicaemia-causing strains (B:2,5, E:2,5, and B:3,4) with an overall accuracy of 96.9 %. Our results suggest that MALDI-TOF MS may be used to routinely screen P. multocida isolated from diagnostic cases for initial identification of haemorrhagic septicaemia-causing strains, and to determine whether additional characterizations are warranted.

First report and genomic characterization of Escherichia coli O111:H12 serotype from raw mussels in Türkiye

BackgroundThis study aimed to assess the prevalence and genomic characteristics of Shiga-toxigenic (STEC) and Enteroaggregative E. coli (EAEC) strains in raw mussels and ready-to-eat (RTE)-stuffed mussels, focusing on potential public health implications for identifying virulence and antimicrobial resistance genes.ResultsThe genome sequence analysis identified the E. coli strain named 23EM as serotype O111:H12, with adhesion (fimH-54) and fumarate hydratase (fumC-11) genes. The draft genome (4.9 Mb, 50.6% GC content, 111 contigs, 4,688 genes) is available in NCBI GenBank (accession JAWXVJ000000000). The strain, classified as ST292 and CC ST10, showed high similarity to nonpathogenic E. coli MG1655 but was distinct from pathogenic strains such as EAEC and ExPEC. In silico serotyping revealed the presence of O111-antigen flippase (wzx) and H12-antigen flagellin (fliC) genes. The strain harbors an IncFII (pCoo) plasmid with 96.95% identity. PathogenFinder predicted a 92% probability of being a human pathogen, supported by 720 pathogenic protein families. CRISPR analysis identified one high-evidence sequence with nine spacers and six low-evidence sequences. Phylogenetic analysis using RAxML positioned 23EM close to nonpathogenic E. coli but distant from other pathogenic strains. Antimicrobial resistance genes across multiple classes, including macrolides, fluoroquinolones, and aminoglycosides, were identified. The strain also contains several virulence factors, such as adhesins (e.g., ECP, ELF, TIF, type IV pili), and autotransporter genes (espP, pic), highlighting its significant pathogenic potential and public health risk.ConclusionsThis study highlights the ability of the detection of E. coli strains harboring virulence and antimicrobial resistance genes in mussels, thus emphasizing the importance of ongoing surveillance and careful consideration of the potential risks associated with the consumption of these shellfish.

Whole-genome sequencing-based genomic characterization of uterine serous carcinoma

Whole-genome sequencing-based genomic characterization of uterine serous carcinoma

Comparative Genomics Reveal Distinct Environment Preference and Functional Adaptation Among Lineages of Gemmatimonadota

Bacteria in the phylum Gemmatimonadota are globally distributed and abundant in microbial communities of various environments, playing an important role in driving biogeochemical cycling on Earth. Although high diversities in taxonomic composition and metabolic capabilities have been reported, little is known about the environmental preferences and associated functional features that facilitate adaptation among different Gemmatimonadota lineages. This study systematically analyzed the relationships between the environments, taxonomy, and functions of Gemmatimonadota lineages, by using a comparative genomics approach based on 1356 Gemmatimonadota genomes (213 high-quality and non-redundant genomes) available in a public database (NCBI). The taxonomic analysis showed that the 99.5% of the genomes belong to the class Gemmatimonadetes, and the rest of the genomes belong to the class Glassbacteria. Functional profiling revealed clear environmental preference among different lineages of Gemmatimonadota, and a marine group and two non-marine groups were identified and tested to be significantly different in functional composition. Further annotation and statistical comparison revealed a large number of functional genes (e.g., amiE, coxS, yfbK) that were significantly enriched in genomes from the marine group, supporting enhanced capabilities in energy acquisition, genetic information regulation (e.g., DNA repair), electrolyte homeostasis, and growth rate control. These genomic features are important for their survival in the marine environment, which is oligotrophic, variable, and with high salinity. The findings enhanced our understanding of the metabolic processes and environmental adaptation of Gemmatimonadota, and further advanced the understanding of the interactions of microorganisms and their habitats.

Genomic characterization and comparative genomics of Chlorella sp. CH2018 from Musi River water, India

Microalgae, a diverse class of photosynthetic eukaryote, can provide food and energy sustainably. Selecting productive strains is crucial for commercial viability. Here, we isolated an axenic microalgal species from Musi River water, and based on its morphology, molecular makeup, and cell wall composition identified it as Chlorella sp. CH2018. Scanning electron microscopy was used to measure the size of cells, which were found to be 3-, 4-, or 5-μm in diameter with a discernible thick outer cell wall. The characterization of algal genomes is imperative for comprehending species, studying metabolic pathways, and modifying genetics. In this study, we sequenced the entire genome of Chlorella sp. CH2018, yielded genome size of 56.83 Mb with 11,143 functionally annotated protein-coding gene models. The Gene Ontology (GO) analysis revealed that Chlorella's predominant metabolic pathway is carbohydrate metabolism. Ortholog comparative analysis of species of phylum Chlorophyta with Chlorella sp. CH2018 showed that the isolated species possesses unique protein families with a maximum number of 6292 ortholog groups with Chlorella sorokiniana. The phylogenetic tree created by concatenating single-copy ortholog sequences demonstrates the uniqueness of Chlorella sp. CH2018, and its genome sequence serves as a genetic resource for future research.

Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programmes and repeats in pluripotent cells.

H3K9me3 heterochromatin, established by lysine methyltransferases (KMTs) and compacted by heterochromatin protein 1 (HP1) isoforms, represses alternative lineage genes and DNA repeats. Our understanding of H3K9me3 heterochromatin stability is presently limited to individual domains and DNA repeats. Here we engineered Suv39h2-knockout mouse embryonic stem cells to degrade remaining two H3K9me3 KMTs within 1 hour and found that both passive dilution and active removal contribute to H3K9me3 decay within 12-24 hours. We discovered four different H3K9me3 decay rates across the genome and chromatin features and transcription factor binding patterns that predict the stability classes. A 'binary switch' governs heterochromatin compaction, with HP1 rapidly dissociating from heterochromatin upon KMT depletion and a particular threshold level of HP1 limiting pioneer factor binding, chromatin opening and exit from pluripotency within 12 h. Unexpectedly, receding H3K9me3 domains unearth residual HP1β peaks enriched with heterochromatin-inducing proteins. Our findings reveal distinct H3K9me3 heterochromatin maintenance dynamics governing gene networks and repeats that together safeguard pluripotency.

Bartonella Species in Small Mammals in Turkey: Bartonella bilalgolemii sp. nov. Isolated from a Ural Field Mouse (Apodemus uralensis).

Background: The genus Bartonella is composed of Gram-negative, fastidious, facultative intracellular bacteria that can cause bacteremia in mammals and various disorders in humans. Rodents have been reported as reservoirs of more than 30 Bartonella species, seven of which cause zoonotic infections. Materials and Methods: In the present study, the isolation of Bartonella sp. was attempted from 150 spleen samples from 13 rodent species (mostly Apodemus species) from three geographically different regions in Turkey. Results: Bartonella sp. was successfully isolated from 65 of these 150 samples (43%). The prevalences of Bartonella sp. in tested rodents in the regions of Giresun, Yozgat, and Burdur were 68%, 44%, and 16%, respectively. Using polymerase chain reaction/sequence analysis of the citrate synthase-coding gene (gltA), Bartonellaisolates were classified seven species including B. taylorii, B. grahamii, B. birtlesii, B. mastomydis, and three putatively new Bartonella species. We performed further identification techniques for one of the three Bartonella species that were different from the validated Bartonella species according to the gltA sequence analysis. Conclusion: Here, we report the genomic and phenotypic characterization of Bartonella sp. strain G70 that was isolated from the splenic tissue of an Apodemus uralensis (Pallas 1881), the Ural field mouse, captured in the Giresun region of northeastern Turkey. Bartonella sp. strainG70 (RSKK 22001) was characterized by whole genome and partial gene (gltA, 16S ribosomal RNA) sequencing and comparison, scanning electron microscopy, biochemical tests, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. This novel Bartonella is a Gram-negative, rod-shaped bacterium and has neither flagella nor pili. The genome from strain G70 was 1,606,969-bp-long with a G + C content of 35.7%. Bartonella rochalimae was found to be the closest phylogenetic relative of strain G70 (OrthoANI = 90.5%, digital DNA-DNA hybridization = 41.4%). We therefore propose that this new species be named Bartonella bilalgolemii sp. nov. with strain G70T as the type strain.

First Detection of High-Level Aminoglycoside-Resistant Klebsiella pneumoniae and Enterobacter cloacae Isolates Due to 16S rRNA Methyltransferases with and Without blaNDM in Uruguay

Background: The increase in antimicrobial resistance includes emerging mechanisms such as 16S ribosomal RNA methylases, which confer high-level resistance to aminoglycosides. In this regard, the most predominant genes observed worldwide are rmtB and armA, but their presence in Uruguay is unknown. Objectives: We describe the genomic characterization of isolates carrying rmtB and rmtC, together with blaNDM-5 and blaNDM-1, respectively, and rmtD in our country. Methology: Five isolates from patients admitted to three hospitals were studied. Identification and antibiotic susceptibility testing were performed using the Vitek2 System. Whole Genome Sequencing was conducted, and hybrid assembly was performed with Unicycler. In silico analysis using the Center for Genomic Epidemiology’s tools was undertaken to predict antibiotic resistance determinants, plasmid incompatibility groups, and sequence types. Results: We report three K. pneumoniae ST307 isolates with an IncR plasmid carrying blaNDM-5/blaCTX-M-15/blaTEM-1B/rmtB/dfrA14/dfrA12/sul1/qacEΔ1/ermB/mphA, one K. pneumoniae ST258 harboring an IncC plasmid containing rmtC/blaNDM-1/blaCMY-6/aac(6′)-Ib/sul1, and one E. cloacae ST88 isolate with an IncFIB/II plasmid hosting rmtD, within a novel Tn21-like transposon named Tn7825, alongside blaOXA-101/sul1/tet(G)/floR, and a new variant of blaTEM assigned as blaTEM-258. One of the strains, named UH_B2, also carried an IncM1 plasmid encoding qnrE1/blaTEM-1/blaCTX-M-8 associated with ISEcp1. Conclusions: This is the first description of plasmids harboring 16S rRNA methyltransferases in Uruguay. The association and dissemination of diverse antibiotic-resistant genes underpin the health threat they represent, highlighting the lack of available antibiotics effective against multidrug-resistant microorganisms.

OHDLF: A Method for Selecting Orthologous Genes for Phylogenetic Construction and Its Application in the Genus Camellia

Accurate phylogenetic tree construction for species without reference genomes often relies on de novo transcriptome assembly to identify single-copy orthologous genes. However, challenges such as whole-genome duplication (WGD), heterozygosity, gene duplication, and loss can hinder the selection of these genes, leading to limited data for constructing reliable species trees. To address these issues, we developed a new analytical pipeline, OHDLF (Orthologous Haploid Duplication and Loss Filter), which filters orthologous genes from transcript data and adapts parameter settings based on genomic characteristics for further phylogenetic tree construction. In this study, we applied OHDLF to the genus Camellia and evaluated its effectiveness in constructing phylogenetic trees. The results highlighted the pipeline’s ability to handle challenges like high heterozygosity and recent gene duplications by selectively retaining genes with a missing rate and merging duplicates with high similarity. This approach ensured the preservation of informative sites and produced a highly supported consensus tree for Camellia. Additionally, we evaluate the accuracy of the OHDLF phylogenetic trees for different species, demonstrating that the OHDLF pipeline provides a flexible and effective method for selecting orthologous genes and constructing accurate phylogenetic trees, adapting to the genomic characteristics of various plant groups.

Complete Chloroplast Genome of Crassula aquatica: Comparative Genomic Analysis and Phylogenetic Relationships

Background/Objectives: Crassula aquatica (L.) Schonl. is a very small annual plant growing along riverbanks. Chloroplast (cp) genomes, crucial for photosynthesis, are highly conserved and play a key role in understanding plant evolution. In this study, we conducted cp genome analysis of C. aquatica, aiming to elucidate its phylogenetic position and structural variations. We analyzed and described the features of the complete cp genome of C. aquatica and conducted comparative analysis with the cp genomes of closely related taxa. Rsults: The cp genome was 144,503 bp in length and exhibited the typical quadripartite structure, consisting of a large single-copy region (LSC; 77,993 bp), a small single-copy region (SSC; 16,784 bp), and two inverted repeats (24,863 bp). The cp genome of C. aquatica comprised 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNA genes. Comparative genomic analysis of 13 other Crassula species and six outgroups demonstrated highly conserved gene content and order among Crassula species. However, notable differences were observed, including the complete loss of the rpoC1 intron in C. aquatica and several closely related species, which may serve as a synapomorphic trait supporting the monophyly of the subgenus Disporocarpa. We analyzed the nucleotide diversity among 14 Crassula cp genomes and identified five highly variable regions (pi > 0.08) in the IGS regions. Phylogenetic analysis based on 78 PCGs confirmed the monophyly of Crassula and its division into two subgenera: Crassula and Disporocarpa. Although the phylogenetic tree supported the subgeneric classification system, the sectional classification system requires reassessment. Conclusions: In this study, we conducted a comparative analysis of the cp genome of the genus Crassula. We inferred evolutionary trends within the Crassula cp genome and provided molecular evidence supporting the integration of the genus Tillaea into the genus Crassula. However, as this study does not represent all species within the genus Tillaea, further comprehensive phylogenetic analyses are requrired.

Developing Anticancer Drug Response System Using Deep Learning System with Hybrid Genomic and Chemical Features

Developing Anticancer Drug Response System Using Deep Learning System with Hybrid Genomic and Chemical Features

Clinicopathologic and Genomic Features of Invasive Stratified Mucin-producing Carcinoma of the Uterine Cervix Coexisting With High-grade Squamous Intraepithelial Lesion.

Invasive stratified mucin-producing carcinoma (ISMC) is a specific type of adenocarcinoma of the cervix, which is associated with human papillomavirus infection and often coexists with other types of carcinomas. However, given its rarity, understanding of this disease remains insufficient. We present a unique case of ISMC of the cervix coexisting with a high-grade squamous intraepithelial lesion (HSIL). In addition to histologic and immunohistochemical feature observation, genomic profiling of the 2 lesions was performed. Histologically, the ISMC and HSIL lesions were independent of each other. Aside from the typical morphology, various architectural features of ISMC were observed. Immunohistochemically, the ISMC and HSIL lesions were strongly and diffusely positive for p16 and exhibited high Ki-67 expression. The ISMC lesion was also positive for CK7, MUC5AC, and MUC6, while it was negative for PAX-8. The HSIL lesion was positive for CK5/6 and p40. The combined positive score of PD-L1 was 55. The other markers were all negative in both lesions, and the p53 was wild-type. Next-generation sequencing analysis revealed multiple gene mutations in the ISMC and HSIL lesions. A total of 88 gene mutations were identified in the ISMC lesion, while 20 gene mutations were identified in the HSIL lesion. Three mutations (ERBB2, histidine decarboxylase gene [HDC], and BSN) were detected in the ISMC and HSIL lesions. Both lesions had a low tumor mutation burden and microsatellite-stable status. No copy number-associated variants or structural variations were identified in either lesion. These results suggest that patients with ISMC may benefit from PD-L1 immunotherapy and targeted therapy.

Genetic and Epigenetic Dysregulation of Transcriptional Enhancers in Cancer

Enhancers are noncoding DNA sequences responsible for orchestrating gene expression programs by interacting with transcription factors and chromatin regulators within complex genome structures. However, their fundamental functions can be disrupted by genetic and epigenetic alterations, leading to aberrant enhancer activation or rewiring that contributes to oncogenesis. Analyzing dysregulated enhancer landscapes reveals new subtype-defining genomic features, such as enhancer hijacking, and identifies disease-relevant transcriptional regulators as potential targets for developing enhancer-targeting therapeutic strategies. Here, we delve into evolving concepts and technologies for studying enhancers; discuss how genetic, epigenetic, and topological alterations disrupt enhancer regulation to promote oncogenic gene expression; and underscore the importance of understanding the regulatory principles governing enhancer function to guide therapeutic strategies. Furthermore, we highlight key challenges and emerging opportunities in targeting enhancers and their regulators to improve cancer classification, prognosis, and treatment.

BakRep - a searchable large-scale web repository for bacterial genomes, characterizations and metadata.

Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding. Meanwhile, access to cost-effective sequencing platforms has accelerated bacterial WGS to unprecedented levels, introducing new challenges in terms of data accessibility, computational demands, heterogeneity of analysis workflows and, thus, ultimately its scientific usability. To this end, a previous study released a uniformly processed set of 661 405 bacterial genome assemblies obtained from the European Nucleotide Archive as of November 2018. Building on these accomplishments, we conducted further genome-based analyses like taxonomic classification, multilocus sequence typing and annotation of all genomes. Here, we present BakRep, a searchable large-scale web repository of these genomes enriched with consistent genome characterizations and original metadata. The platform provides a flexible search engine combining taxonomic, genomic and metadata information, as well as interactive elements to visualize genomic features. Furthermore, all results can be downloaded for offline analyses via an accompanying command line tool. The web repository is accessible via https://bakrep.computational.bio.

Genomic characterization of a clonal emergent Salmonella Minnesota lineage in Brazil reveals the presence of a novel megaplasmid of resistance and virulence.

Salmonella Minnesota has emerged in Brazil as the predominant serovar in poultry and poultry products, along with Salmonella Heidelberg. To understand the emergence of Salmonella Minnesota over the last few years in Brazil, we performed a comparative analysis between 69 selected S. Minnesota genomes from Pathogen Detection database and 65 clonal emergent genomes isolated from Brazil. We demonstrate the presence of multidrug resistance genes against tetracycline [tet(A)], sulfonamide (sul2), and AmpC beta-lactamase (blaCMY-2) in emergent genomes, along with the carriage of a megaplasmid of resistance and virulence (~210 kb), designated pESM (plasmid for emergent Salmonella Minnesota). pESM is an IncC/A2 plasmid predicted to increase S. Minnesota environmental tolerance to mercury (mer operon) and provide resistance to tetracycline and ampicillin due to the presence of tet(A) and blaCMY-2, respectively. Moreover, pESM carries the yersiniabactin siderophore (high-pathogenicity island of Yersinia) related to the iron uptake. The temporal inference demonstrated that the most recent common ancestor dated from ~1978 and that the clonal emergent genomes carrying the pESM belong to a completely different lineage of S. Minnesota. Our results indicate that the presence of pESM likely contributes to the emergence of S. Minnesota and is precisely related to the successful spread of this particular clonal lineage in Brazil.IMPORTANCESalmonella Minnesota has emerged in Brazil as one of the leading serovars related to human and animal infection, presenting high virulence and antibiotic resistance to drugs classified as the highest priority for clinical treatment in humans. This study performed whole-genome sequencing, temporal analysis, and phylogenetics to understand the genetic insights related to the emergence of Salmonella Minnesota in Brazil. Long-read sequencing has led to the identification and characterization of a unique megaplasmid carrying virulence, antibiotic resistance, and heavy-metal tolerance genes, which may play a central role in S. Minnesota's successful emergence in Brazil and possibly worldwide. The potentially high transmissibility of this plasmid between clones and serovars represents a risk to public health since its acquisition may increase Salmonella's fitness, virulence, resistance, and persistence. Understanding the genetic aspects related to the emergence of serovars can help devise measures to mitigate the spread of hazardous multidrug-resistant strains.

Identification of a newly discovered virus from Culex and Armigeres mosquitoes in China

Mosquito associated virus have always been a significant threat to global health. Metagenomics offers a straightforward and quantitative means to acquire the information of novel virus and has greatly enriched the content of mosquito associated virus databases. During an entomological surveillance for arthropod-borne viruses in China, we identified a previously unrecognized virus from mosquitoes, temporarily named Huajieling virus. In this study, a total of 3,960 mosquitoes were collected and then divided into 91 pools, according to location and species. QRT-PCR and nested PCR were performed to confirm the presence of Huajieling virus. Its genomic features and phylogenetic relationships were further analyzed. Our results showed that Huajieling virus was detected in 7 of the 91 mosquito pools and that the minimum infection rate (MIR) was 0.18% (7/3,960). One complete genome sequence and 2 viral partial sequences were obtained from the Huajieling virus-positive pools. Pairwise distances analysis indicated that these amplified sequences shared high nucleotide identity. Phylogenetic analysis demonstrated that Huajieling virus is most closely related to Wufeng shrew picorna-like virus 43, which belonging to Picornavirales. Further analyses indicated that Huajieling virus is a new member of unclassified Picornavirales, and is intermediate between the family Caliciviridae and Secoviridae in taxonomic status.