scholarly journals Comprehensive Virulence Gene Profiling of Bovine Non-aureusStaphylococci Based on Whole-Genome Sequencing Data

mSystems ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Sohail Naushad ◽  
S. Ali Naqvi ◽  
Diego Nobrega ◽  
Christopher Luby ◽  
John P. Kastelic ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Virulence Factors ◽  
Immune Evasion ◽  
Severe Disease ◽  
Virulence Gene ◽  
Gene Profiling ◽  
Whole Genome Sequencing Data ◽  
Functional Categories ◽  
Sequencing Data ◽  
Vf Gene

ABSTRACTNon-aureusstaphylococci (NAS) are the most frequently isolated pathogens from intramammary infection (IMI) in dairy cattle. Virulence factors (VFs) and mechanisms by which NAS cause IMI are not fully known. Herein, we analyzed the distribution of 191 VFs in 441 genomes of 25 NAS species, after classifying VFs into functional categories: adherence (n = 28), exoenzymes (n = 21), immune evasion (n = 20), iron metabolism (n = 29), and toxins (n = 93). In addition to establishing VF gene profiles, associations of VF genes between and among functional categories were computed, revealing distinctive patterns of association among VFs for various NAS species. Associations were also computed for low, medium, and high somatic cell count (SCC) and clinical mastitis (CM) isolates, demonstrating distinctive patterns of associations for low SCC and CM isolates, but no differences between high SCC and CM isolates. To determine whether VF distributions had any association with SCC or CM, various clustering approaches, including complete linkages, Ward clustering, and t-distributed stochastic neighbor embedding, were applied. However, no clustering of isolates representing low SCC, medium SCC, or high SCC or CM was identified. Regression analysis to test for associations with individual VF functional categories demonstrated that each additional toxin and host immune evasion gene increased the odds of having high SCC or CM, although an overall increase in the number of VFs was not associated with increased SCC or occurrence of CM. In conclusion, we established comprehensive VF gene profiling, determined VF gene distributions and associations, calculated pathogenic potentials of all NAS species, and detected no clear link between VF genes and mastitis.IMPORTANCENon-aureusstaphylococci (NAS) are the most frequently isolated pathogens from milk in dairy cattle worldwide. The virulence factors (VFs) and mechanisms by which these bacteria cause udder infection are not fully known. We determined the distribution and associations of 191 VFs in 25 NAS species and investigated the relationship between VFs and disease. Although the overall number of VFs was not associated with disease severity, increasing numbers of toxin and host immune evasion genes specifically were associated with more severe disease outcomes. These findings suggest that the development of disease and the interactions of VFs with the host are complex and determined by the interplay of genes rather than just the presence of virulence genes. Together, our results provide foundational genetic knowledge to other researchers to design and conduct further experiments, focusing on understanding the synergy between VFs and roles of individual NAS species in IMI and characterizing species-specific effects on udder health.

scholarly journals Evaluation of variant identification methods for whole genome sequencing data in dairy cattle

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 948 ◽  
Author(s):  
Christine F Baes ◽  
Marlies A Dolezal ◽  
James E Koltes ◽  
Beat Bapst ◽  
Eric Fritz-Waters ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Identification Methods ◽  
Variant Identification

scholarly journals Molecular Characterization Reveals Similar Virulence Gene Content in Unrelated Clonal Groups of Escherichia coli of Serogroup O174 (OX3)

2007 ◽  
Vol 190 (4) ◽  
pp. 1344-1349 ◽  
Author(s):  
Cheryl L. Tarr ◽  
Adam M. Nelson ◽  
Lothar Beutin ◽  
Katharina E. P. Olsen ◽  
Thomas S. Whittam
Keyword(s):  
Escherichia Coli ◽  
Severe Disease ◽  
Virulence Gene ◽  
Gene Profiling ◽  
Gene Content ◽  
Farm Animals ◽  
Shiga Toxins ◽  
E Coli ◽  
Uremic Syndrome ◽  
Enterocyte Effacement

ABSTRACT Most severe illnesses that are attributed to Shiga toxin-producing Escherichia coli are caused by isolates that also carry a pathogenicity island called the locus of enterocyte effacement (LEE). However, many cases of severe disease are associated with LEE-negative strains. We characterized the virulence gene content and the evolutionary relationships of Escherichia coli isolates of serogroup O174 (formerly OX3), strains of which have been implicated in cases of hemorrhagic colitis and hemolytic uremic syndrome. A total of 56 isolates from humans, farm animals, and food were subjected to multilocus virulence gene profiling (MVGP), and a subset of 16 isolates was subjected to multilocus sequence analysis (MLSA). The MLSA revealed that the O174 isolates fall into four separate evolutionary clusters within the E. coli phylogeny and are related to a diverse array of clonal groups, including enteropathogenic E. coli 2 (EPEC 2), enterohemorrhagic E. coli 2 (EHEC 2), and EHEC-O121. Of the 15 genes that we surveyed with MVGP, only 6 are common in the O174 strains. The different clonal groups within the O174 serogroup appear to have independently acquired and maintained similar sets of genes that include the Shiga toxins (stx 1 and stx 2) and two adhesins (saa and iha). The absence of certain O island (OI) genes, such as those found on OI-122, is consistent with the notion that certain pathogenicity islands act cooperatively with the LEE island.

scholarly journals 1046. Clinical and Microbiological Characteristics of Patients With Septicemia Caused by IMP-1-Producing Enterobacteriaceae in a Tertiary Hospital in Japan

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S312-S313
Author(s):  
Nobuaki Mori ◽  
Narito Kagawa ◽  
Kotaro Aoki ◽  
Yoshikazu Ishii ◽  
Kazuhiro Tateda ◽  
...  
Keyword(s):  
Severe Disease ◽  
Previous History ◽  
Genomic Analysis ◽  
Underlying Disease ◽  
Tertiary Hospital ◽  
Mercaptoacetic Acid ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Microbiological Characteristics

Abstract Background Carbapenemase-producing Enterobacteriaceae (CPE) infection has become a great threat to public health worldwide. Although KPC and OXA-48 infections have mostly described, IMP-1 producing Enterobacteriaceae (IMP1-E) are not well studied. We investigated the clinical and microbiological characteristics of septicemia due to the IMP1-E. Methods This observational study of inpatients who developed IMP-1E septicemia was conducted in a Japanese tertiary hospital from April 2013 to March 2017. IMP1-E was defined as a decreased susceptibility to meropenem (minimum inhibitory concentration, ≥2 mg/L), as well as a positive sodium mercaptoacetic acid test, and polymerase chain reaction for blaIMP genes. Clinical data were collected from medical charts. Antimicrobial susceptibilitly was determined by the MicroScan Walkway. We performed total genomic analysis, plasmid analysis, and multilocus sequence typing (MLST) using whole genome sequencing data. Results In total, six patients were identified (median age: 55 years). All had severe underlying disease on admission, and five were admitted to the intensive care unit. The sources of IMP1-E septicemia were as follows: two catheter-related BSI, one pyelonephritis, one cholangitis, one bacterial peritonitis, and one unknown focus. Four isolates were Enterobacter cloacae and two were Klebsiella pneumoniae. All patients had a previous history of antibiotic treatment and long-term hospitalization. All patients were treated with either levofloxacin (LVFX) only or LVFX and aminoglycoside (AG). Follow-up blood culture was negative for all patients. All-cause 30-day mortality rate was 50%. Although no isolates were resistant to LVFX and AG, they harbored aac(6’)-Ⅱc, sul1, and tet(B) genes.Two isolates harbored the qnrB6 gene. There was a high probability that blaIMP-1 was carried by IncHI2 plasmids. MLST sequence type of E. cloacae isolates comprised three ST78, and one ST997; K. pneumonia isolates comprised ST134, and ST252. Conclusion This study showed that IMP1-E septicemia was isolated in patients with severe disease and long-term hospitalization. Selection of antibiotics therapy based on antimicrobial susceptibility induced microbiological cure, but clinical response was dependent on the underlying diseases. Disclosures All authors: No reported disclosures.

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract

2021 ◽  
Author(s):  
Johanna L. Jones ◽  
Mark A. Corbett ◽  
Elise Yeaman ◽  
Duran Zhao ◽  
Jozef Gecz ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Protein Interactions ◽  
Cholesterol Biosynthesis ◽  
Crystalline Lens ◽  
Whole Genome Sequencing Data ◽  
Mendelian Disease ◽  
Cataract Formation ◽  
Sequencing Data ◽  
Zebrafish Model ◽  
Paediatric Cataract

AbstractInherited paediatric cataract is a rare Mendelian disease that results in visual impairment or blindness due to a clouding of the eye’s crystalline lens. Here we report an Australian family with isolated paediatric cataract, which we had previously mapped to Xq24. Linkage at Xq24–25 (LOD = 2.53) was confirmed, and the region refined with a denser marker map. In addition, two autosomal regions with suggestive evidence of linkage were observed. A segregating 127 kb deletion (chrX:g.118373226_118500408del) in the Xq24–25 linkage region was identified from whole-genome sequencing data. This deletion completely removed a commonly deleted long non-coding RNA gene LOC101928336 and truncated the protein coding progesterone receptor membrane component 1 (PGRMC1) gene following exon 1. A literature search revealed a report of two unrelated males with non-syndromic intellectual disability, as well as congenital cataract, who had contiguous gene deletions that accounted for their intellectual disability but also disrupted the PGRMC1 gene. A morpholino-induced pgrmc1 knockdown in a zebrafish model produced significant cataract formation, supporting a role for PGRMC1 in lens development and cataract formation. We hypothesise that the loss of PGRMC1 causes cataract through disrupted PGRMC1-CYP51A1 protein–protein interactions and altered cholesterol biosynthesis. The cause of paediatric cataract in this family is the truncating deletion of PGRMC1, which we report as a novel cataract gene.

scholarly journals Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhongbo Chen ◽  
◽  
David Zhang ◽  
Regina H. Reynolds ◽  
Emil K. Gustavsson ◽  
...  
Keyword(s):  
Neurological Diseases ◽  
Purifying Selection ◽  
Whole Genome Sequencing Data ◽  
Human Lineage ◽  
Sequencing Data ◽  
Protein Coding ◽  
Potential Association ◽  
High Depth ◽  
Specific Sequences ◽  
Human Specific

AbstractKnowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. We find that CNCRs are depleted from protein-coding genes but enriched within lncRNAs. We demonstrate that per-SNP heritability of a range of brain-relevant phenotypes are enriched within CNCRs. We find that genes implicated in neurological diseases have high CNCR density, including APOE, highlighting an unannotated intron-3 retention event. Using human brain RNA-sequencing data, we show the intron-3-retaining transcript to be more abundant in Alzheimer’s disease with more severe tau and amyloid pathological burden. Thus, we demonstrate potential association of human-lineage-specific sequences in brain development and neurological disease.

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