Whole genome characterization of Neisseria meningitidis serogroup W isolates, circulating in Moscow

Introduction. The invasive meningococcal disease (meningitis and/or septicemia) is actual problem of public health in Russia. Neisseria meningitidis isolates are classified into serogroups, PorA/FetA VRs, sequence types and clonal complexes. The growth of the invasive forms of meningococcal infection caused by isolates with «W: P1.5,2: F1-1: ST-11 (cc11)» profile requires attention for extended genotyping because the discriminating ability of classical MLST and antigens typing does not allow to answer the question about genetic and antigenic features of the pathogens and their epidemic potential. Materials and Methods. Four N. meningitidis serogroup W isolates associated with invasive meningococcal disease in Moscow (Russia) were characterized by next-generation sequencing. Three isolates were sequenced directly from cerebrospinal fluid samples and one -as a bacterial culture. All isolates were characterized earlier and the data were published in the PubMLST data base (id38565, id38573, id50225 and id50241). Genomic DNA was sequenced on Illumina MiSeq instrument. Results and Discussion. Obtained sequences allowed us to characterize four meningococci isolates for more than 1400 loci from the core genome MLST scheme. We have analyzed the core genome MLST scheme information about surface-antigen coding sequences. Housekeeping genes sequences were used to determine eMLST profile, ribosomal protein genes and some antibiotic resistance associated genes. We have characterized some ribosomal protein genes and antibiotic resistance associated genes. Based on eMLST profiles we noticed that there are at list two clones of N. meningitidis serogroup W inside complex ST-11/ET-37 clonal complex circulating in Moscow during 2016. An eMLST profile of isolates id50225 and id50241 differs in 3 loci out of 20. Application of the approach based on next-generation sequencing in routine epidemiological surveillance dramatically increases the amount of data and genotyping discriminating ability.

Neisseria meningitidis, серогруппа W, менингококковая инфекция, генерализованные формы менингококковой инфекции, мультилокусное секвенирование-типирование, клональный комплекс, массовое параллельное секвенирование, расширенное МЛСТ, Neisseria meningitidis, serogroup W, meningococcal infection, multilocus sequence typing, clonal complex, next-generation sequencing, core genome, extended MLST

1. Jolley K.A, Brehony C., Maiden M.C.J. Molecular typing of meningococci: recommendations for target choice and nomenclature. FEMS microbiology reviews. 2007; 31 (1): 89 – 96.

2. Mironov K. O. Clonal complex of Neisseria meningitidis, circulating in the regions of Russia and their role in epidemic process of meningococcal infection. Epidemiologia i Infekcionnie Bolezni. Aktualnie Problemi. [Epidemiology and Infection Diseases. Current Items]. 2016; (6): 52 – 61 (in Russian).

3. Matosova S. V., Mironov K. O., Platonov A. E., Shipulina O.Yu., Nagibina M.V., Vengerov Yu.Ya., et al. Molecular biological monitoring of Neisseria meningitidis in Moscow in the period 2011 to 2015. Epidemiologia i Infekcionnie Bolezni. Aktualnie Problemi. [Epidemiology and Infection Diseases. Current Items]. 2016; (2): 4–9 (in Russian).

4. Matosova S.V., Mironov K.O., Smirnova V.S., Shipulina O.Yu., Nagibina M.V., Chernyshov D.V. et al. The distribution of Neisseria meningitidis serogroups causing the generalized forms of meningococcal infection in Moscow during 2016. Proceedings of 9th All-Russia Research and Practical Conference with international participation «Molecular diagnostics 2017». Moscow; 2017. 240 – 241 (in Russian).

5. Mironov K.O., Platonov A.E., Dribnokhodova O.P., Kuseva V.I., Shipulin G.A. A method for determination of Neisseria meningitides serogroup A, B, C and W by real-time PCR. Zhurnal Mikrobioligii. [Journal of Microbiology]. 2014; (6): 35 – 42 (in Russian).

6. Kostyukova N.N., Bekhalo V.A., Chernyshova T.F. Meningococcal infection in Russia: The past and the immediate prospects. Epidemiologia i Infekcionnie Bolezni. Aktualnie Problemi. [Epidemiology and Infection Diseases. Current Items]. 2014; (2): 73–79 (in Russian).

7. Ivanova M.V., Skripchenko N.V., Vilnits A. A., Gorelik E. Y., Matyunina N. V., Serednyakov K. V. The Course of generalized meningococcal infection caused by meningococcus serogroup W135. Detskie infekcii. [Children Infections]. 2016; 15 (4): 57 – 60 (in Russian).

8. Mironov K.O., Zhivotova V.A., Matosova S.V., Shipulina O.Yu., Markelov M.L., Goptar I.A. et al. Genotyping of Neisseria meningitides causing the generalized forms of meningococcal infection in Moscow during 2016. Proceedings of 9th All- Russia Research and Practical Conference with international participation «Molecular diagnostics 2017». Moscow; 2017. 223 – 225 (in Russian).

9. Bratcher H. B., Corton C., Jolley K.A., Parkhill J., Maiden M.C.J. A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC genomics. 2014; 15: 1138.

10. Mustapha M.M., Marsh J.W., Harrison L.H. Global epidemiology of capsular group W meningococcal disease (1970 – 2015): Multifocal emergence and persistence of hypervirulent sequence type (ST)-11 clonal complex. Vaccine. 2016; 34 (13): 1515 – 1523.

11. Okonechnikov K., Conesa A., García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2015; btv566.

12. García-Alcalde F., Okonechnikov K., Carbonell J., Cruz L.M., Götz S., Tarazona S. et al. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics. 2012; 28 (20): 2678 – 2679.

13. Fiebelkorn K.R., Crawford S.A., Jorgensen J.H. Mutations in folP Associated with Elevated Sulfonamide MICs for Neisseria meningitidis Clinical Isolates from Five Continents. Antimicrobial Agents and Chemotherapy. 2005; 49 (2): 536 – 540.

14. Jolley K.A., Maiden M. C.J. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC bioinformatics. 2010; 11: 595.

15. Inouye M., Dashnow H., Raven L.-A., Schultz M.B., Pope B.J., Tomita T. et al. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Medicine. 2014; 6 (11): 90.

16. Maiden M.C., Bygraves J.A., Feil E., Morelli G., Russell J.E., Urwin R. et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proceedings of the National Academy of Sciences of the United States of America. 1998; 95 (6): 3140 – 3145.

17. Cherkasskiy B.L. Globalnaya epidemiologiya. Global epidemiology. Moscow: Prakticheskaya Medicina; 2008. 447 (in Russian).