Detailed molecular characterization of Neisseria meningitidis isolates by whole genome sequencing (WGS), Czech Republic, 2010–2019
Authors:
M. Honskus; Z. Okonji; M. Musílek; P. Křížová
Authors‘ workplace:
Národní referenční laboratoř pro meningokokové nákazy, Centrum epidemiologie a mikrobiologie, Státní zdravotní ústav, Praha
Published in:
Epidemiol. Mikrobiol. Imunol. 70, 2021, č. 3, s. 168-177
Category:
Original Papers
Overview
Aim: Presentation of the first results of the analysis of Neisseria meningitidis isolates from invasive meningococcal disease and from clinically and/or epidemiologically linked cases from 2010–2019. Whole genome sequencing (WGS) was used for the study.
Material and methods: The study set included 59 isolates of N. meningitidis from 2010–2019. Serogrouping was done by conventional serological methods and confirmed by RT-PCR. WGS was used for detailed molecular characterization, covering not only basic genes but also ribosomal and capsular genes, antibiotic resistance gene penA, and outer membrane protein gene porA.
Results: WGS analysis of N. meningitidis isolates resulted in a detailed molecular characterization. In a large part of the genes analysed, new mutated allelic variants were found. They were submitted to the PubMLST database and subsequently annotated by the curator. All 59 study isolates were assigned to BAST types, characterized by a unique combination of allelic variants of N. meningitidis B vaccine (MenB vaccine) antigen genes. Overall, 32 different BAST types were identified, and 10 isolates either carried an unknown combination of BAST loci or a new allelic variant in some of the BAST loci. Furthermore, the MenDeVAR index, which provides information on the functional effect of MenB vaccines on a given isolate, was determined.
Conclusions: The results obtained add to the body of knowledge of the transmission of invasive and non-invasive strains of N. meningitidis in the population. The WGS analysis provided detailed data on the coverage of these strains by new MenB vaccines.
Keywords:
Neisseria meningitidis – whole genome sequencing (WGS)
Sources
1. Caugant DA, Brynildsrud OB. Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis. Nat Rev Microbiol, 2020;18(2):84–96. DOI:10.1038/s41579-019-0282-6.
2. Jolley KA, Wilson DJ, Kriz P, et al. The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis. Mol Biol Evol, 2005;22(3):562–569. DOI:10.1093/molbev/msi041.
3. Feil EJ, Enright MC, Spratt BG. Estimating the relative contributions of mutation and recombination to clonal diversification: a comparison between Neisseria meningitidis and Streptococcus pneumoniae. Res Microbiol, 2000;151(6):465–946. DOI:10.1016/ s0923-2508(00)00168-6.
4. Brehony C, Rodrigues CMC, Borrow R, et al. Distribution of Bexsero ® Antigen Sequence Types (BASTs) in invasive meningococcal disease isolates: Implications for immunisation. Vaccine, 2016;34(39):4690–4697. DOI:10.1016/j.vaccine.2016.08.015.
5. https://pubmlst.org/organisms/neisseria-spp/
6. Maiden MCJ, Bygraves JA, Feil E, et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA, 1998;95(6):3140–3145. DOI:10.1073/pnas.95.6.3140.
7. Brehony C, Jolley KA, Maiden MCJ. Multilocus sequence typing for global surveillance of meningococcal disease. FEMS Microbiol Rev, 2007;31(1):15–26. DOI:10.1111/j.1574- 6976.2006.00056.x.
8. Jolley KA, Maiden MCJ. Using multilocus sequence typing to study bacterial variation: prospects in the genomic era. Future Microbiol, 2014;9(5):623–630. DOI:10.2217/fmb.14.24.
9. PCR for Detection and Characterization of Bacterial Meningitis Pathogens: Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae, in Laboratory Methods for the Diagnosis of Meningitis caused by Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae, CDC manual, Chapter
10. Dostupné na www: https://www.cdc.gov/meningitis/ lab-manual/chpt10-pcr.html. 10. Manuál QIAamp DNA Mini Kit. Dostupné na www: http:// www.qiagen.com/Products/Catalog/Sample-Technologies/ DNA-Sample-Technologies/Genomic-DNA/ QIAamp-DNA-Mini-Kit#technicalspecification.
11. Zerbino DR. Using the Velvet de novo assembler for shortread sequencing technologies. Curr Protoc Bioinformatics, 2010;11(11.5). DOI:10.1002/0471250953.bi1105s31.
12. Jolley KA, Maiden MCJ. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics, 2010;11:595. DOI:10.1186/1471-2105-11-595.
13. Harrison OB, Claus H, Jiang, et al. Description and Nomenclature of Neisseria meningitidis Capsule Locus. Emerg Infect Dis, 2013;19(4):566–573. DOI:10.3201/eid1904.111799.
14. Marjuki H, Topaz N, Rodriguez-Rivera LD, et al. Whole-Genome Sequencing for Characterization of Capsule Locus and Prediction of Serogroup of Invasive Meningococcal Isolates. J Clin Microbiol, 2019;57(3). DOI: 10.1128/JCM.01609-18.
15. Jolley KA, Brehony C, Maiden MCJ. Molecular typing of meningococci: recommendations for target choice and nomenclature. FEMS Microbiol Rev, 2007;31(1):89–96. DOI: 10.1111/j.1574- 6976.2006.00057.x.
16. Jolley KA, Bliss CM, Bennett JS, et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology (Reading), 2012;158(4):1005–1015. DOI: 10.1099/mic.0.055459-0.
17. Rodrigues ChMC, Jolley KA, Smith A, et al. Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index: a Rapid and Accessible Tool That Exploits Genomic Data in Public Health and Clinical Microbiology Applications. J Clin Microbiol, 2020;59(1). DOI: 10.1128/JCM.02161-20.
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Hygiene and epidemiology Medical virology Clinical microbiologyArticle was published in
Epidemiology, Microbiology, Immunology
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