scholarly journals Whole genome sequencing of Neisseria meningitidis W isolates from the Czech Republic recovered in 1984 – 2017

2018 ◽  
Author(s):  
Michal Honskus ◽  
Zuzana Okonji ◽  
Martin Musilek ◽  
Jana Kozakova ◽  
Pavla Krizova
Keyword(s):  
Czech Republic ◽  
Neisseria Meningitidis ◽  
Clonal Complex ◽  
Vaccine Antigen ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
The Czech Republic ◽  
Vaccine Potential ◽  
Healthy Carriers

AbstractIntroductionThe study presents the analysis of whole genome sequence (WGS) data for Neisseria meningitidis serogroup W isolates recovered in the Czech Republic in 1984 – 2017 and their comparison with WGS data from other countries.Material and MethodsThirty-one Czech N. meningitidis W isolates, 22 from invasive meningococcal disease (IMD) and nine from healthy carriers were analysed. The 33-year study period was divided into three periods: 1984-1999, 2000-2009, and 2010-2017.ResultsMost study isolates from IMD and healthy carriers were assigned to clonal complex cc22 (n = 10) in all study periods. The second leading clonal complex was cc865 (n = 8) presented by IMD (n = 7) and carriage (n = 1) isolates that emerged in the last study period, 2010 – 2017. The third clonal complex was cc11 (n = 4) including IMD isolates from the first (1984 – 1999) and third (2010 – 2017) study periods. The following clonal complex was cc174 (n = 3) presented by IMD isolates from the first two study periods, i.e. 1984 – 1999 and 2000 – 2009. One isolate of each cc41/44 and cc1136 originated from healthy carriers from the second study period, 2000 - 2009. The comparison of WGS data for N. meningitidis W isolates recovered in the Czech Republic in the study period 1984 – 2017 and for isolates from other countries recovered in the same period showed that clonal complex cc865, ST-3342 is unique to the Czech Republic since 2010. Moreover, the comparison shows that cc11 in the Czech Republic does not comprise novel hypervirulent lineages reported from both European and non-European countries. WGS data for Czech serogroup W meningococci point to the presence of MenB vaccine antigen genes and confirm the hypothesis about the MenB vaccine potential against N. meningitidis serogroup W. All 31 study isolates were assigned to Bexsero® Antigen Sequence Types (BAST), and seven of them were of newly described BASTs.ConclusionsWGS analysis contributed considerably to a more detailed molecular characterization of N. meningitidis W isolates recovered in the Czech Republic over a 33-year period and allowed for a spatial and temporal comparison of these characteristics between isolates from the Czech Republic and other countries. In addition, the WGS data precised the base for the update of the recommendation for vaccination in the Czech Republic.

scholarly journals Determination of serotyping antigens, clonal analysis and genetic characterization of the 4CMenB vaccine antigen genes in invasive Neisseria meningitidis from Western Canada, 2009 to 2013

2014 ◽  
Vol 63 (11) ◽  
pp. 1490-1499 ◽  
Author(s):  
Dennis K. S. Law ◽  
Jianwei Zhou ◽  
Saul Deng ◽  
Linda Hoang ◽  
Gregory Tyrrell ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Clonal Complex ◽  
Factor H ◽  
Vaccine Antigen ◽  
Western Canada ◽  
Antigenic Analysis ◽  
Clonal Nature ◽  
4Cmenb Vaccine

This study examined invasive Neisseria meningitidis recovered from invasive meningococcal disease (IMD) cases in Western Canada between 2009 and 2013. A total of 161 isolates from individual IMD cases were analysed for serogroup, serotype, serosubtype, PorA genotype, multi-locus sequence type and nucleotide sequence of their 4CMenB vaccine antigen genes. Sixty-nine isolates were serogroup B (MenB), 47 were serogroup Y (MenY), 22 were serogroup C (MenC), 19 were serogroup W (MenW), three were serogroup E and one was non-encapsulated. MenC, MenY and MenW were mainly clonal, represented primarily by clonal complex (cc) 11, cc23 or cc167, and cc22, respectively. In contrast, MenB were composed of eight different ccs together with 11 isolates not assigned to any known cc. Antigenic analysis and PorA genotyping confirmed the heterogeneity of MenB isolates, while such results supported the clonal nature of most MenC, MenY and MenW isolates. Thirty-four (21.1 %) isolates had at least one gene that encoded one matching vaccine protein component of the 4CMenB vaccine (i.e. PorA P1.4; fHbp variant 1.1; NHBA peptide 2; and NadA-1, -2, or -3). An additional 18 isolates had genes that encoded variant 1 or subfamily B factor H binding proteins of this same vaccine.

scholarly journals Whole genome sequencing of Neisseria meningitidis W isolates from the Czech Republic recovered in 1984–2017

PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0199652 ◽  
Author(s):  
Michal Honskus ◽  
Zuzana Okonji ◽  
Martin Musilek ◽  
Jana Kozakova ◽  
Pavla Krizova
Keyword(s):  
Czech Republic ◽  
Neisseria Meningitidis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
The Czech Republic

scholarly journals Whole-Genome Sequence of an African Swine Fever Virus Isolate from the Czech Republic

2020 ◽  
Vol 9 (44) ◽  
Author(s):  
Jan H. Forth ◽  
Leonie F. Forth ◽  
Petr Václavek ◽  
Pavel Barták ◽  
Dirk Höper ◽  
...  
Keyword(s):  
Czech Republic ◽  
Genome Sequence ◽  
Virus Isolate ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
High Identity ◽  
The Czech Republic ◽  
Very High

ABSTRACT Between June 2017 and April 2018, an outbreak of African swine fever (ASF) affected wild boar in the southeast of the Czech Republic. Here, we present the whole-genome sequence of the causative ASF virus. It belongs to genotype II and shows very high identity with other strains from Eastern Europe.

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

scholarly journals SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weili Cai ◽  
Schyler Nunziata ◽  
John Rascoe ◽  
Michael J. Stulberg
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Coverage ◽  
Metagenomic Sample ◽  
Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

scholarly journals Whole-Genome Sequence of Multidrug-ResistantPseudomonas aeruginosaStrain BAMCPA07-48, Isolated from a Combat Injury Wound

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Fatemeh Sanjar ◽  
S. L. Rajasekhar Karna ◽  
Tsute Chen ◽  
Ping Chen ◽  
Johnathan J. Abercrombie ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Valuable Resource ◽  
Combat Injury ◽  
Pathogen Surveillance

We report here the complete genome sequence ofPseudomonas aeruginosastrain BAMCPA07-48, isolated from a combat injury wound. The closed genome sequence of this isolate is a valuable resource for pathogenome characterization ofP. aeruginosaassociated with wounds, which will aid in the development of a higher-resolution phylogenomic framework for molecular-guided pathogen-surveillance.

scholarly journals Increase in meningococcal disease associated with the emergence of a novel ST-11 variant of serogroup C Neisseria meningitidis in Victoria, Australia, 1999–2000

2002 ◽  
Vol 128 (1) ◽  
pp. 7-14 ◽  
Author(s):  
D. E. TRIBE ◽  
A. M. ZAIA ◽  
J. M. GRIFFITH ◽  
P. M. ROBINSON ◽  
H. Y. LI ◽  
...  
Keyword(s):  
Czech Republic ◽  
Dna Sequencing ◽  
Neisseria Meningitidis ◽  
Meningococcal Disease ◽  
Age Distribution ◽  
Housekeeping Gene ◽  
Restriction Pattern ◽  
The Novel ◽  
Age Group ◽  
The Czech Republic

In the years 1999–2000, there was an increase in the incidence of meningococcal disease in Victoria, largely caused by Neisseria meningitidis serogroup C. This change was associated with a shift in age distribution of cases, with relatively more disease appearing in the 15–29 year age group, and with 40/58 serogroup C isolates in 2000 exhibiting a new macrorestriction pattern (pattern A). Thirty-four of 52 pattern A isolates tested displayed the novel phenotype C:2a:P1.4, and were consistently porA VR type P1.7-2,4 by DNA sequencing. Nine of 10 representative pattern A isolates analysed displayed a housekeeping gene allele profile (ST-11) that is characteristic of the electrophoretic type (ET)-15 variant that has caused outbreaks in Canada, the Czech Republic and Greece. Meningococci belonging to the ST-11 complex that were isolated in Victoria prior to 1999 did not display either restriction pattern A or PorA VR type P1.7-2,4.

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