scholarly journals IdentifyingStreptococcus pneumoniaegenes associated with invasive disease using pangenome-based whole genome sequence typing

2018 ◽  
Author(s):  
Uri Obolski ◽  
Andrea Gori ◽  
José Lourenço ◽  
Craig Thompson ◽  
Robin Thompson ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Pneumococcal Disease ◽  
Learning Algorithm ◽  
Invasive Disease ◽  
Whole Genome Sequence ◽  
Data Sets ◽  
Whole Genome ◽  
Upper Respiratory Tract ◽  
Pneumococcal Carriage ◽  
Upper Respiratory

AbstractStreptococcus pneumoniaeis a normal commensal of the upper respiratory tract but can also invade the bloodstream or CSF (cerebrospinal fluid), causing invasive pneumococcal disease (IPD). In this study, we attempt to identify genes associated with IPD by applying a random forest machine-learning algorithm to whole genome sequence (WGS) data. We find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of these genes, 23 genes have previously shown to be directly relevant to IPD, while the other 18 are uncharacterized.

scholarly journals First Complete Genome Sequence of Haemophilus influenzae Serotype a

2017 ◽  
Vol 5 (3) ◽  
Author(s):  
Mariam Iskander ◽  
Kristy Hayden ◽  
Gary Van Domselaar ◽  
Raymond Tsang
Keyword(s):  
Haemophilus Influenzae ◽  
Genome Sequence ◽  
Invasive Disease ◽  
Indigenous Populations ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Human Pathogen ◽  
Small Children ◽  
Content Type ◽  
Serotype A

ABSTRACT Haemophilus influenzae is an important human pathogen that primarily infects small children. In recent years, H. influenzae serotype a has emerged as a significant cause of invasive disease among indigenous populations. Here, we present the first complete whole-genome sequence of H. influenzae serotype a.

scholarly journals First Whole-Genome Sequence of a Haemophilus influenzae Type e Strain Isolated from a Patient with Invasive Disease in Italy

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Maria Giufrè ◽  
Rita Cardines ◽  
Marina Cerquetti
Keyword(s):  
Haemophilus Influenzae ◽  
Genome Sequence ◽  
Invasive Disease ◽  
Whole Genome Sequence ◽  
Haemophilus Influenzae Type ◽  
Whole Genome ◽  
Type B ◽  
Genomic Information ◽  
Conjugate Vaccines ◽  
Content Type

ABSTRACT In the present era of conjugate vaccines against Haemophilus influenzae type b, non-vaccine-preventable strains are of concern. Here, we report the first whole-genome sequence of an invasive H. influenzae type e strain. This genomic information will enable further investigations on encapsulated non-type b H. influenzae strains.

scholarly journals Mining Whole Genome Sequence data to efficiently attribute individuals to source populations

2020 ◽  
Author(s):  
Francisco J. Pérez-Reche ◽  
Ovidiu Rotariu ◽  
Bruno S. Lopes ◽  
Ken J. Forbes ◽  
Norval J.C. Strachan
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Large Data ◽  
Biological Species ◽  
Whole Genome Sequence ◽  
Data Sets ◽  
Whole Genome ◽  
Computationally Efficient ◽  
Proteomic Data ◽  
Source Populations

ABSTRACTWhole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that effectively mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application.

scholarly journals RNA Sequencing Data Sets and Their Whole-Genome Sequence Assembly of Dengue Virus from Three Serial Passages in Vero Cells

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Thidathip Wongsurawat ◽  
Nuntaya Punyadee ◽  
Piroon Jenjaroenpun ◽  
Dumrong Mairiang ◽  
Nattaya Tangthawornchaikul ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Rna Sequencing ◽  
Genome Sequence ◽  
Vero Cells ◽  
Sequence Assembly ◽  
Whole Genome Sequence ◽  
Data Sets ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genome Sequence Assembly

ABSTRACT We present RNA sequencing data sets and their genome sequence assembly for dengue virus that was isolated from a patient with dengue hemorrhagic fever and serially propagated in Vero cells. RNA sequencing data obtained from the first, third, and fifth passages and their corresponding whole-genome sequences are provided in this work.

scholarly journals 90Factors associated with pneumococcal carriage in children and adults in Fiji, using four cross-sectional surveys

2021 ◽  
Vol 50 (Supplement_1) ◽  
Author(s):  
Eleanor Neal ◽  
Cattram Nguyen ◽  
Felista Tupou Ratu ◽  
Eileen Dunne ◽  
Mike Kama ◽  
...  
Keyword(s):  
Pneumococcal Disease ◽  
Cigarette Smoke Exposure ◽  
Upper Respiratory Tract ◽  
Urban Residence ◽  
Cross Sectional ◽  
Factors Associated ◽  
Pneumococcal Carriage ◽  
Upper Respiratory ◽  
Using Data ◽  
Coverage Rates

Abstract Background Pneumococcal disease is preceded by carriage of pneumococci. We describe factors associated with pneumococcal nasopharyngeal carriage in Fiji, using data from annual (2012-2015) cross-sectional surveys, pre- and post-introduction of ten-valent pneumococcal conjugate vaccine (PCV10). Methods Infants (5-8 weeks), toddlers (12-23 months), children (2-6 years), and their caregivers participated. Pneumococci were detected using lytA qPCR, with molecular serotyping by microarray. We used logistic regression to determine predictors of carriage and density. Results There were 8,109 participants. Pneumococcal carriage was associated with: years post-PCV10 introduction (global P<0.001), iTaukei ethnicity (aOR 2.74 [95% CI 2.17-3.45] P<0.001); young age (global P<0.001); urban residence (aOR 1.45 [95% CI 1.30-2.57] P<0.001); living with >2 children <5 years (aOR 1.42 [95% CI 1.27-1.59] P<0.001); poverty (aOR 1.44 [95% CI 1.28-1.62] P<0.001); and upper respiratory tract infection (URTI) symptoms (aOR 1.77 [95% CI 1.57-2.01] P<0.001). Factors associated with PCV10 and non-PCV10 carriage were similar to those associated with overall carriage. Additionally, PCV10 carriage was associated with PCV10 vaccination (0.58 [95% CI 0.41-0.82] P=0.002) and cigarette smoke exposure (aOR 1.21 [95% CI 1.02-1.43] P=0.031. Non-PCV10 carriage was not associated with years post-PCV10 introduction. Conclusions Introduction of PCV10 reduced the odds of overall and PCV10 pneumococcal carriage in Fiji. ITaukei ethnicity was positively associated with carriage after adjustment for PCV10. Key messages PCV10 introduction was associated with reduced odds of overall and PCV10 pneumococcal carriage in Fiji. Despite high and similar PCV10 coverage rates, iTaukei ethnicity is positively associated with pneumococcal carriage, compared with Fijian of Indian Descent populations.

Whole-Genome Sequence Characterization of Primary Auxin-Responsive Aux/IAA Gene Family in Sorghum (Sorghum bicolor L.)

2010 ◽  
Vol 36 (4) ◽  
pp. 688-694
Author(s):  
Yi-Jun WANG ◽  
Yan-Ping LÜ ◽  
Qin XIE ◽  
De-Xiang DENG ◽  
Yun-Long BIAN
Keyword(s):  
Sorghum Bicolor ◽  
Gene Family ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Characterization ◽  
I Gene
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